Auto-tuned nested parallelism: A way to reduce the execution time of scientific software in NUMA systems

The most computationally demanding scientific problems are solved with large parallel systems. In some cases these systems are Non-Uniform Memory Access (NUMA) multiprocessors made up of a large number of cores which share a hierarchically organized memory. The main basic component of these scientific codes is often matrix multiplication, and the efficient development of other linear algebra packages is directly based on the matrix multiplication routine implemented in the BLAS library. BLAS library is used in the form of packages implemented by the vendors or free implementations. The latest versions of this library are multithreaded and can be used efficiently in multicore systems, but when they are used inside parallel codes, the two parallelism levels can interfere and produce a degradation of the performance. In this work, an auto-tuning method is proposed to select automatically the optimum number of threads to use at each parallel level when multithreaded linear algebra routines are called from OpenMP parallel codes. The method is based on a simple but effective theoretical model of the execution time of the two-level routines. The methodology is applied to a two-level matrix–matrix multiplication and to different matrix factorizations (LU, QR and Cholesky) by blocks. Traditional schemes which directly use the multithreaded routine of BLAS, dgemm, are compared with schemes combining the multithreaded dgemm with OpenMP.     

Effects of a single dose of beetroot juice on cycling time trial performance at ventilatory thresholds intensity in male triathletes

Background

Beetroot juice (BJ) is classified as a high-level supplement for improving sports performance. There is some controversy over the benefits of BJ supplementation for endurance exercise performance, especially when referring to well-trained athletes. This study examines the effects of acute BJ supplementation on cardioventilatory responses, exercise economy/efficiency, slow component of oxygen uptake, time trial performance, blood lactate, energy consumption, and carbohydrate and fat oxidation.

Methods

Twelve well-trained, male triathletes (aged 21–47 yr) were assigned in a randomized, double-blind, crossover design to receive 70 ml of BJ (6.5 mmol NO₃^?) or placebo (PL). Three hours after taking the supplement, participants completed an endurance test on a cycle ergometer at a constant work rate (W) corresponding to first ventilatory threshold (VT1) (30 min) and second ventilatory threshold (VT2) time trial (~?15 min).

Results

Maximal oxygen uptake was 54.78?±?3.13 mL·min^??1·kg^??1, and gross efficiency was >?22% at each load intensity and experimental condition. No significant interaction effect (supplement*intensity) was observed on any of the cardioventilatory variables, efficiency/economy, VT2 time trial, energy expenditure, carbohydrate oxidation and fat oxidation (p?>?0.05).

Conclusion

Our findings do not support an improvement in the variables examined in response to acute BJ supplementation. Probably, higher doses are needed for improving time trial performance in male triathletes during a cycle ergometer test conducted at a load intensity equivalent to the first and second ventilatory threshold.

     

Catalyst layer optimization by surface tension control during ink formulation of membrane electrode assemblies in proton exchange membrane fuel cell

A cost effective production of the membrane electrode assemblies (MEA) is a crucial issue for the generation of electricity by proton exchange membrane fuel cells (PEMFC). The deposition of the exact catalyst content on the electrodes in a single printing step is desirable to save processing time and enable cost reduction. In this study, an innovative MEA production process by screen print is developed to produce high performance catalyst layers. The control of the surface tension of the catalyst ink is fundamental to allow the catalyst layer deposition in a single printing step. The electrodes prepared in this way show higher performance than those prepared in several steps. The optimal ink developed shows a viscosity of 2.75 Pa s, a total solid content of 33.76 wt.%, a density of 1.294 g cm⁻³, and tack value of 92 U.T.     

Rheological and Microstructural Characterization of Wheat Dough Formulated with High Levels of Resistant Starch

Fiber-enriched breads can contribute to increasing the daily fiber intake. Resistant starches (RS) are a useful resource to increase the amount of non-digestible carbohydrates while preserving as far as possible the technological quality of white bread. The effects of high concentrations of Hi-Maize (HM), a type 2 RS, in dough formulations were analyzed by farinograph, dynamic rheometric assays, texture profile analysis, and ¹H-NMR relaxation measurements and related to particle size and microstructural characteristics studied by different microscopy techniques (SEM, ESEM, CLSM). Up to 30% replacement with HM was performed. Water absorption increased and development time and stability decreased when the amount of HM increased. Water mobility increased suggesting a change in water binding. The mechanical spectra indicated a prevalence of the solid-like character in all samples, but the G′ (storage modulus) vs. G″ (loss modulus) plot suggested a pronounced change in the microstructure of dough at the highest level of replacement. Dough was harder, more adhesive, and less resilient when the HM content was increased. The use of HM in the premix formulations not only diluted the gluten content but also changed the size particle distribution of starch granules by increasing the fraction with smaller sizes. Thus, more compact matrices were obtained with a noticeable disruption of the gluten network at the highest level of replacement. However, an intermediate level of RS addition (20%) still rendered a dough with satisfactory rheological properties for breadmaking.     

Fabrication of ferrogels using different magnetic nanoparticles and their performance on protein adsorption

Magnetic biomaterials were prepared using magnetite and chitosan‐coated magnetite nanoparticles (CSNPs) dispersed in poly(vinyl alcohol) gels. Two different methods were developed to obtain ferrogels: in situ co‐precipitation of magnetite (Ferro‐IS) and by adding previously synthesized CSNPs to the neat matrix (Ferro‐CSNPs). In both cases, the crosslinking was carried out by freezing ? thawing (F‐T). The as‐prepared materials as well as precursor CSNPs were characterized by Fourier transform infrared spectroscopy, electronic microscopy (scanning and transmission), X‐ray diffraction, ζ potential, dynamic light scattering, thermogravimetric analysis, differential scanning calorimetry and magnetic properties. The performance of these gels as protein adsorbents was evaluated. Batch adsorption experiments were carried out using bovine serum albumin (BSA) as a model. Substantially different adsorption behaviour was found using Ferro‐IS and Ferro‐CSNPs. This was assigned to dissimilar bonding mechanisms of BSA to the ferrogel matrix. Hence, biomaterials potentially useful in drug delivery as well as in protein purification fields may be prepared by a relatively simple, non‐toxic and low cost method. © 2013 Society of Chemical Industry     

PARCSIM: a parallel computing simulator for scalable software optimization

The Journal of Supercomputing - PARCSIM is a parallel software simulator that allows a user to capture, through a graphical interface, matrix algorithm schemes that solve scientific problems. With...     

Investigation of gaseous ozone as an anti‐fungal fumigant for stored wheat

In this study, gaseous ozone was used as a fungicide to preserve stored wheat. The following operating parameters were investigated for their effects on the fungicidal efficacy of ozone: (1) the applied ozone dose; (2) ozonation time; (3) water activity of the wheat; and (4) temperature of the wheat. The effect of ozonation on germination of the wheat was also studied. Experimental results revealed that gaseous ozone was very effective in the inactivation of fungi associated with the wheat. Within 5 min of ozonation, 96.9% of the fungal spores were inactivated by applying 0.33 mg of ozone (g wheat)^?1 min^?1. It was also found that increases in both water activity and temperature of the wheat enhanced the fungicidal efficacy of ozone. In addition, results of this study indicated that the inactivation processes could be controlled by simply monitoring the ozone exiting from the reactor and, consequently, the time‐consuming microbial examination processes could be avoided. This finding would make the application of ozone in the preservation of cereal grains easier, simpler, and more cost‐effective. It was also found that although the applied ozone doses above certain thresholds may reduce the germination of wheat, the inactivation of fungi could be achieved using applied ozone doses far below those thresholds. Copyright © 2006 Society of Chemical Industry     

Chylous ascites following heart transplantation

BACKGROUND: Hepatocellular carcinoma is highly refractory to most chemotherapeutic agents. Clofazimine, a riminophenazine compound used to treat leprosy since 1962, inhibits various cancer cell lines, including hepatocellular carcinoma cell lines, via phospholipase A2 dependant processes. Clofazimine also inhibits p170-glycoprotein, the mdr1 gene product. PATIENTS AND METHODS: Thirty patients (26 males and four females) with unresectable (25) or metastatic (5) hepatocellular carcinoma received oral clofazimine 600 mg daily for two weeks, followed by 400 mg daily until progression or death. RESULTS: There were three responses (10%)--one of a soft tissue metastasis, and two of local disease, with 13 patients disease stabilizing for up to 20 months. The overall median survival was 13 weeks. Adverse events included hyperpigmentation, eczematous skin rashes and palpitations. CONCLUSIONS: Although only three patients had an objective response (10%), the 13 patients with stable disease for up to 20 months, and an overall median survival of 13 weeks, suggest that clofazimine, or other riminophenazine compounds may prove to be of value in hepatocellular carcinoma.     

Size‐controlled gold nanoparticles inside polyacrylamide microgels

Gold nanoparticles (AuNPs) of different sizes were synthesized into a crosslinked network of polyacrylamide (PAAm) microgels. PAAm was prepared by means of semicontinuous inverse heterophase polymerization under monomer‐starving conditions with a z‐average particle size of 384 ± 18 nm. AuNPs with controlled size were obtained by a reduction reaction of Au⁺³ to Au⁰ from a gold(III) chloride trihydrate (HAuCl₄) solution inside microgel the crosslinked network (AuNP‐PAAm). The reduction reaction was verified for 2 h by ultraviolet–visible spectroscopy (UV–vis). AuNP–PAAm exhibited a particle size between 288 ± 12 and 230 ± 15 nm at HAuCl₄ concentrations of 0.4 and 1.3 mM, respectively. The AuNP–PAAms were observed by transmission electron microscopy, and their sizes were determined to be 19 ± 2 nm (1.3 mM) and 17 ± 2 nm (1.1 mM). With UV–vis spectroscopy, we detected the formation of AuNPs at a wavelength of 552 nm, and with X‐ray diffraction analysis, we proved that the crystal arrangement was face‐centered cubic. © 2016 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2016 , 133, 43560.