Evaluating kernels on Xeon Phi to accelerate Gysela application

This work describes the challenges presented by porting parts ofthe Gysela code to the Intel Xeon Phi coprocessor, as well as techniques used for optimization, vectorization and tuning that can be applied to other applications. We evaluate the performance of somegeneric micro-benchmark on Phi versus Intel Sandy Bridge. Several interpolation kernels useful for the Gysela application are analyzed and the performance are shown. Some memory-bound and compute-bound kernels are accelerated by a factor 2 on the Phi device compared to Sandy architecture. Nevertheless, it is hard, if not impossible, to reach a large fraction of the peek performance on the Phi device,especially for real-life applications as Gysela. A collateral benefit of this optimization and tuning work is that the execution time of Gysela (using 4D advections) has decreased on a standard architecture such as Intel Sandy Bridge.Comment: submitted to ESAIM proceedings for CEMRACS 2014 summer school version reviewe

Biofortification of staple crops to eliminate human malnutrition: contributions and potential in developing countries

Micronutrient malnutrition is a global health challenge affecting almost half of the global population, causing poor physical and mental development of children and a wide range of illnesses. It is most prevalent in young girls, women, and pre-school children who are suffering particularly from the low consumption of vitamins and micronutrients. Given this global challenge, biofortification has proven to be a promising and economical approach to increase the concentration of essential micronutrients in edible portions of staple crops. Produce quality and micronutrient content can be further enhanced with the use of micronutrient fertilizers. Especially developing countries with a high percentage of malnourished populations are attracted to this integrated biofortification, combining modern agronomic interventions and genetic improvement of food crops. Consequently, maize, rice, wheat, beans, pearl millet, sweet potato, and cassava have all been biofortified with increased concentrations of Fe, Zn, or provitamin A in various developing countries. Today, there are several large-scale success stories in Africa and Asia that support the research and development of biofortified crops. In this review, we summarized what has been achieved to date and how edible crops can be further improved by integrating agronomic and genetic strategies to upgrade the nutritional status of children and adults around the world

Nutrient Management for Higher Productivity of Swarna Sub1 Under Flash Floods Areas

Two field experiments were conducted at Regional Agricultural Research Station, Tarahara, Nepal during 2012 and 2013 to determine the effect of agronomic management on growth and yield of Swarna Sub1 under flash floods. The first experiment was laid out in a split plot design with three replications; and four different nutrient combinations at nursery as main plots and three age groups of rice seedlings as sub plots. The second experiment was laid out in a randomized complete block design and replicated thrice; with three post flood nutrient doses at six and 12 days after de-submergence (dad). The experiments were complete submerged at 10 days after transplanting for 12 days. The survival percentage, at 21 dad, was significantly higher in plots planted with 35 (90.25%) and 40 (91.58%) days-old seedlings compared to 30 days-old seedlings (81.75%). Plots with 35 days-old seedlings produced 5.15 t ha-1 with advantage of 18.83% over 30 days-old seedlings. Plots with 100-50-50 kg N-P2O5-K2O/ha at nursery recorded the highest grain filling of 79.41% and grain yield of 5.068 t/ha with more benefit. Post flood application of 20-20 N-K20kg/ha at 6 dad resulted in higher plant survival and taller plants, leading to significantly higher grain yield of 5.183 t/ha and straw yield of 5.315 t/ha. Hence, 35-40 days old seedlings raised with 100-50-50 kg N-P2O5-K2O /ha in nursery and the additional application of20-20 kg N-K2O /ha at 6 dad improved plant survival and enhanced yield of Swarna Sub1 under flash flood conditions. The practice has prospects of saving crop loss with getting rice yield above national average yield leading to enhanced food security in the flood prone areas of Nepal

Regional differences in nitrogen balance and nitrogen use efficiency in the rice–livestock system of Uruguay

The reintegration of crops with livestock systems is proposed as a way of improving the environmental impacts of food production globally, particularly the impact involving nitrogen (N). A detailed understanding of processes governing N fluxes and budgets is needed to design productive and efficient crop–livestock systems. This study aimed to investigate regional differences in N balance (NBAL, defined as all N inputs minus outputs), N use efficiency (NUE, defined as N outputs/inputs × 100), and N surplus (NSURP, defined as all N inputs minus only outputs in food products) in the rice–livestock system of Uruguay. Three regions across Uruguay are distinguished based on soil fertility and length of pasture rotation. The northern region has high soil fertility and short length of rotation (HFSR); the central region has medium soil fertility and medium length of rotation (MFMR); the eastern region has low fertility and long pasture rotation (LFLR). Results for the last 18 years show a very high NUE (90%) for the rice component in all rotations, associated with negative NBALs ranging from −35 kg N ha−1 yr−1 in HFSR to −3 kg N ha−1 yr−1 in LFLR. However, the livestock component, which overall had low animal productivity (<2 kg N ha−1 yr−1), had low NUE (<10%) but positive NBALs in all the rotations, sustaining N supply in the rice component. At the system level, NUE was high (60%) and NBAL was slightly positive in all rotations (from +2.8 kg N ha−1 yr−1 in HFSR to +8.5 kg N ha−1 yr−1 in LFLR). Because of a recent increase in the N fertilizer dose in rice, NSURP for the overall system was intermediate (40 kg N ha−1 yr−1) and should be monitored in the future. Efforts to improve the system's efficiency should focus on the livestock component

Spectral soil analysis for fertilizer recommendations by coupling with QUEFTS for maize in East Africa: A sensitivity analysis

Laboratory analysis of soil properties is prohibitively expensive and difficult to scale across the soils in sub Saharan Africa. This results in a lack of soil-specific fertilizer recommendations, where recommendation can only be provided at a regional scale. This study aims to assess the feasibility of using spectral soil analysis to provide soil-specific fertilizer recommendations. Using a range of spectrometers [NeoSpectra Saucer (NIR), FieldSpec 4 (vis-NIR) with contact probe or mug light interface, FTIR Bruker Tensor 27 (MIR)], 346 archived soil samples (0–20 cm) with known soil chemical properties collected from Ethiopia, Kenya and Tanzania were scanned. Partial least square regression (PLSR) was used to develop prediction models for selected soil properties including pH, soil organic carbon (SOC), total nitrogen, Olsen P, and exchangeable K. These predicted properties, and associated uncertainty, were used to derive fertilizer recommendations for maize using the Quantitative Evaluation of the Fertility of Tropical Soils (QUEFTS) model parameters for sub-Saharan Africa. Most soil properties (pH, SOC, total nitrogen, and exchangeable K) were well predicted (Concordance Correlation Coefficient values between 0.88 and 0.96 and Ratio of Performance to Interquartile values between 1.4 and 5.9) by all the spectrometers but there were performance variations between soil properties and spec- trometers. Use of the predicted soil data for the development of fertilizer recommendations gave promising results when compared to the recommendations obtained with the conventional soil analysis. For example, the least performing NeoSpectra Saucer over/under-estimated up to 8 and 24 kg ha-1N and P, respectively, though there was insignificant variation in estimation of P fertilizer among spectrometers. We conclude that spectral technology can be used to determine major soil properties with satisfactory precision, sufficient for specific fertilizer decision making in East Africa, possibly even with portable equipment in the fiel

Transcriptional Network Involved in Drought Response and Adaptation in Cereals

Drought is the major abiotic stress in many wheat environments, decreasing grain yields and farmer’s income. Finding ways to improve drought tolerance in wheat is therefore a global effort. Transcription factors (TFs) play important roles in drought tolerance by stimulating plant’s protective genome activities in response to heat and water limitation. TFs are specialized proteins which can bind to specific DNA elements in gene promoters and modulate gene expression in response to various external and internal stimuli. Thus TFs is a crucial part of plant signal transduction pathway mediated by signal receptors, phytohormones and other regulatory compounds. The activities of TFs are closely related to their structure, and their binding specificity is determined by the homo-/hetero-dimerization of TFs. The expression of downstream genes may produce a subset of TFs or regulate other functional proteins involved in physiological drought adaptation. Thus, the hierarchic regulations of TF activities, downstream gene expression and protein–protein interaction comprise a complex regulatory network, which participates in drought response and adaptation in cereal crops. Basic mechanisms of this regulatory network have been described, but more insight is needed to find new tools for enhancing cereals’ adaptation to drought stress

The soil organic carbon: Clay ratio in North Devon, UK: Implications for marketing soil carbon as an asset class

Building up stocks of agricultural soil organic carbon (SOC) can improve soil conditions as well as contribute to climate change mitigation. As a metric, the ratio of SOC to clay offers a better predictor of soil condition than SOC alone, potentially providing a benchmark for ecosystem service payments. We determined SOC:clay ratios for 50 fields in the North Devon UNESCO World Biosphere Reserve using 30 cm soil cores (divided into 0-10 cm and 10-30 cm depth samples), with soil bulk density, soil moisture and land-use history recorded for each field. All the arable soils exceeded the minimum desirable SOC:clay ratio threshold, and the ley grassland soils generally exceeded it but were inconsistent at 10-30 cm. Land use was the primary factor driving SOC:clay ratios at 0-10 cm, with permanent pasture fields having the highest ratios followed by ley grass and then arable fields. Approximately half of the fields sampled had potential for building up SOC stock at 10-30 cm. However, at this depth, the effect of land use is significantly reduced. Within-field variability in SOC and clay was low (coefficient of variation was similar to 10%) at both 0-10 cm and 10-30 cm, suggesting that SOC:clay ratios precisely characterized the fields. Due to the high SOC:clay ratios found, we conclude that there is limited opportunity to market additional carbon sequestration as an asset class in the North Devon Biosphere or similar areas. Instead, preserving existing SOC stocks would be a more suitable ecosystem service payment basis

A comparison of soil texture measurements using mid-infrared spectroscopy (MIRS) and laser diffraction analysis (LDA) in diverse soils

Spectroscopic methods for the determination of soil texture are faster and cheaper than the standard methods, but how do the results compare? To address this question, laser diffraction analysis (LDA) and mid-infrared spectroscopy (MIRS) analysis have been compared to conventional sieve-pipette measurements of texture in diverse European and Kenyan soils. To our knowledge this comparison between LDA and MIRS has not been made previously. It has used soils with a broad range of organic carbon (OC) contents to investigate whether, as in other techniques, clay-OC aggregation affects the estimation of clay with MIRS. The MIRS predictions of clay content were much better than the LDA measurements, but both techniques gave good measurements of sand content. The MIRS over-estimated clay at low clay content and under-estimated at high clay content (calibration set R2 = 0.83). The LDA over-estimated clay by ~ 60% (calibration set R2 = 0.36), indicating that the widely used clay threshold of  5% OC the LDA under-estimated (R2 =  < 0.1) and MIRS over-estimated (R2 = 0.34) clay content. In soils with OC removed, the MIRS prediction of clay content improved, indicating interference between over-lapping spectral regions for organic and mineral constituents. Unlike granulometric measurements of texture such as the LDA, MIRS analysis is not subject to the limitations imposed by the shape and density of particles. It was concluded that in typical agricultural soils with < 5% OC and < 60% clay content, both techniques could be used for cheap, fast and reliable estimates of soil texture

The distribution of soil micro-nutrients and the effects on herbage micro-nutrient uptake and yield in three different pasture systems

Pasture micro-nutrient concentrations are often deficient for herbage productivity and the health of livestock. The aim of this study was to investigate soil and herbage micro-nutrient content and the effects on yield on the three pasture systems of the North Wyke Farm Platform (NWFP): high-sugar grass + legume mix minus nitrogen (N) fertilizer (blue/HSG + L); permanent pasture plus N fertilizer (green/P + N); high-sugar grass plus N fertilizer (red/HSG + N). The locations with high soil total micro-nutrient concentrations had a greater slope and higher soil organic matter (SOM) content. Herbage micro-nutrient concentrations were often greater at the locations with high soil total micro-nutrient concentrations. The concentration and uptake of nearly all mi-cro-nutrients was greatest in the herbage of the green/P + N system, which had the highest SOM content, whereas they were often lowest in the red/HSG + N system, which had the lowest SOM and the highest yield, indicating biomass dilution of micro-nutrients in the herbage. At the loca-tions with high soil micro-nutrient concentrations, yield was higher than at locations with low micro-nutrient concentrations, and was equal across the three pasture systems, regardless of fertilizer N treatment. Variation in micro-nutrient uptake/yield in the blue grass–legume system was predominantly explained by the soil molybdenum (Mo) concentration, possibly relating to the requirement for Mo in biological nitrogen fixation. There was, therefore, a trade-off in ploughing and re-seeding for higher yield, with the maintenance of SOM being important for herbage micro-nutrient content