Experiences in porting mini-applications to OpenACC and OpenMP on heterogeneous systems

This article studies mini-applications—Minisweep, GenASiS, GPP, and FF—that use computational methods commonly encountered in HPC. We have ported these applications to develop OpenACC and OpenMP versions, and evaluated their performance on Titan (Cray XK7 with K20x GPUs), Cori (Cray XC40 with Intel KNL), Summit (IBM AC922 with Volta GPUs), and Cori-GPU (Cray CS-Storm 500NX with Intel Skylake and Volta GPUs). Our goals are for these new ports to be useful to both application and compiler developers, to document and describe the lessons learned and the methodology to create optimized OpenMP and OpenACC versions, and to provide a description of possible migration paths between the two specifications. Cases where specific directives or code patterns result in improved performance for a given architecture are highlighted. We also include discussions of the functionality and maturity of the latest compilers available on the above platforms with respect to OpenACC or OpenMP implementations

Parallel Unsmoothed Aggregation Algebraic Multigrid Algorithms on GPUs

We design and implement a parallel algebraic multigrid method for isotropic graph Laplacian problems on multicore Graphical Processing Units (GPUs). The proposed AMG method is based on the aggregation framework. The setup phase of the algorithm uses a parallel maximal independent set algorithm in forming aggregates and the resulting coarse level hierarchy is then used in a K-cycle iteration solve phase with a $\ell^1$-Jacobi smoother. Numerical tests of a parallel implementation of the method for graphics processors are presented to demonstrate its effectiveness.Comment: 18 pages, 3 figure

Ultraviolet Imaging Polarimetry of the Large Magellanic Cloud. II. Models

Motivated by new sounding-rocket wide-field polarimetric images of the Large Magellanic Cloud, we have used a three-dimensional Monte Carlo radiation transfer code to investigate the escape of near-ultraviolet photons from young stellar associations embedded within a disk of dusty material (i.e. a galaxy). As photons propagate through the disk, they may be scattered or absorbed by dust. Scattered photons are polarized and tracked until they escape to be observed; absorbed photons heat the dust, which radiates isotropically in the far-infrared, where the galaxy is optically thin. The code produces four output images: near- UV and far-IR flux, and near-UV images in the linear Stokes parameters Q and U. From these images we construct simulated UV polarization maps of the LMC. We use these maps to place constraints on the star + dust geometry of the LMC and the optical properties of its dust grains. By tuning the model input parameters to produce maps that match the observed polarization maps, we derive information about the inclination of the LMC disk to the plane of the sky, and about the scattering phase function g. We compute a grid of models with i = 28 deg., 36 deg., and 45 deg., and g = 0.64, 0.70, 0.77, 0.83, and 0.90. The model which best reproduces the observed polarization maps has i = 36 +2/-5 degrees and g ~0.7. Because of the low signal-to-noise in the data, we cannot place firm constraints on the value of g. The highly inclined models do not match the observed centro-symmetric polarization patterns around bright OB associations, or the distribution of polarization values. Our models approximately reproduce the observed ultraviolet photopolarimetry of the western side of the LMC; however, the output images depend on many input parameters and are nonunique.Comment: Accepted to AJ. 20 pages, 7 figure

Influence of crop residue ration supplementation on the attainment of puberty and postpartum reproductive activities of Red Sokoto goats

The general objective of this study was to come up with an appropriate, affordable and locally available crop residue supplementation package that would enhance reproductive performance in small ruminants. Specifically, 28 Red Sokoto weaner does between 3 and 4 months of age weighing between 2 and 3 kg were used in the first experiment to determine the influence of crop residue supplementation on age and weight at puberty as determined by blood progesterone levels. In the second experiment, another 28 adult does (equal to or greater than 2 years old) of the same breed in the same flock with lactation numbers between 1 and 3 were used to determine the length of postpartum acyclic period. In both experiments, a 3 x 2 factorial experimental design comprising three dietary supplements (A, B, C) at two feeding levels (1% and 2% of body weight) fed in addition to a basal diet of Digitaria smutsii hay and natural pasture ad libitum with an unsupplemented negative control group (D) and four goats per treatment was utilized. In ration A, a conventional concentrate supplement consisting of maize, wheat offal, cottonseed cake and bonemeal was utilized; in rations B and C, the supplement consisted of guinea-corn bran, cowpea husk and groundnut haulms; and maize offal, groundnut shells and groundnut haulms respectively. Unsupplemented (ration D) weaner does reached puberty at a later age and had lighter body weights than all the others. Weaner does on ration 2A (concentrate fed at 2% of body weight) attained puberty at the earliest age and heaviest body weight, although the age at puberty was not significantly different from those on rations 1A (concentrate fed at 1% body weight), 1C and 2C. Blood progesterone profiles before and after puberty ranged from 0.05 to 9.0 ng/ml, respectively, and was highest in does fed rations A and C and least in the unsupplemented does. The mean interval between kidding and initiation of ovarian activity was 54.28 plus or minus 17.61 days and the mean interval between kidding and conception was 63.04 plus or minus 25.34 days. Only 25% of the unsupplemented does conceived again during the period under study compared with 100% in rations 1A, 2A, 1C and 2C; 75% in ration 2B and 50% in ration 1B. It was concluded that implementation of supplementary feeding in the dry season improves reproductive performance in the Red Sokoto doe. Furthermore, ration C, a crop residue-based ration, was a suitable dry season supplementation alternative to the expensive conventional concentrate ration for the smallholder goat farmer in the subhumid tropics of Nigeria

Superconductivity in Fullerides

Experimental studies of superconductivity properties of fullerides are briefly reviewed. Theoretical calculations of the electron-phonon coupling, in particular for the intramolecular phonons, are discussed extensively. The calculations are compared with coupling constants deduced from a number of different experimental techniques. It is discussed why the A_3 C_60 are not Mott-Hubbard insulators, in spite of the large Coulomb interaction. Estimates of the Coulomb pseudopotential $\mu^*$, describing the effect of the Coulomb repulsion on the superconductivity, as well as possible electronic mechanisms for the superconductivity are reviewed. The calculation of various properties within the Migdal-Eliashberg theory and attempts to go beyond this theory are described.Comment: 33 pages, latex2e, revtex using rmp style, 15 figures, submitted to Review of Modern Physics, more information at http://radix2.mpi-stuttgart.mpg.de/fullerene/fullerene.htm

Tips for implementing multigrid methods on domains containing holes

As part of our development of a computer code to perform 3D `constrained evolution' of Einstein's equations in 3+1 form, we discuss issues regarding the efficient solution of elliptic equations on domains containing holes (i.e., excised regions), via the multigrid method. We consider as a test case the Poisson equation with a nonlinear term added, as a means of illustrating the principles involved, and move to a "real world" 3-dimensional problem which is the solution of the conformally flat Hamiltonian constraint with Dirichlet and Robin boundary conditions. Using our vertex-centered multigrid code, we demonstrate globally second-order-accurate solutions of elliptic equations over domains containing holes, in two and three spatial dimensions. Keys to the success of this method are the choice of the restriction operator near the holes and definition of the location of the inner boundary. In some cases (e.g. two holes in two dimensions), more and more smoothing may be required as the mesh spacing decreases to zero; however for the resolutions currently of interest to many numerical relativists, it is feasible to maintain second order convergence by concentrating smoothing (spatially) where it is needed most. This paper, and our publicly available source code, are intended to serve as semi-pedagogical guides for those who may wish to implement similar schemes.Comment: 18 pages, 11 figures, LaTeX. Added clarifications and references re. scope of paper, mathematical foundations, relevance of work. Accepted for publication in Classical & Quantum Gravit

Ultra-Rapid Categorization of Fourier-Spectrum Equalized Natural Images: Macaques and Humans Perform Similarly

BACKGROUND: Comparative studies of cognitive processes find similarities between humans and apes but also monkeys. Even high-level processes, like the ability to categorize classes of object from any natural scene under ultra-rapid time constraints, seem to be present in rhesus macaque monkeys (despite a smaller brain and the lack of language and a cultural background). An interesting and still open question concerns the degree to which the same images are treated with the same efficacy by humans and monkeys when a low level cue, the spatial frequency content, is controlled. METHODOLOGY/PRINCIPAL FINDINGS: We used a set of natural images equalized in Fourier spectrum and asked whether it is still possible to categorize them as containing an animal and at what speed. One rhesus macaque monkey performed a forced-choice saccadic task with a good accuracy (67.5% and 76% for new and familiar images respectively) although performance was lower than with non-equalized images. Importantly, the minimum reaction time was still very fast (100 ms). We compared the performances of human subjects with the same setup and the same set of (new) images. Overall mean performance of humans was also lower than with original images (64% correct) but the minimum reaction time was still short (140 ms). CONCLUSION: Performances on individual images (% correct but not reaction times) for both humans and the monkey were significantly correlated suggesting that both species use similar features to perform the task. A similar advantage for full-face images was seen for both species. The results also suggest that local low spatial frequency information could be important, a finding that fits the theory that fast categorization relies on a rapid feedforward magnocellular signal

ESC core curriculum for the general cardiologist (2013)

[No abstract available

Revival of the magnetar PSR J1622-4950: observations with MeerKAT, Parkes, XMM-Newton, Swift, Chandra, and NuSTAR

New radio (MeerKAT and Parkes) and X-ray (XMM-Newton, Swift, Chandra, and NuSTAR) observations of PSR J1622-4950 indicate that the magnetar, in a quiescent state since at least early 2015, reactivated between 2017 March 19 and April 5. The radio flux density, while variable, is approximately 100x larger than during its dormant state. The X-ray flux one month after reactivation was at least 800x larger than during quiescence, and has been decaying exponentially on a 111+/-19 day timescale. This high-flux state, together with a radio-derived rotational ephemeris, enabled for the first time the detection of X-ray pulsations for this magnetar. At 5%, the 0.3-6 keV pulsed fraction is comparable to the smallest observed for magnetars. The overall pulsar geometry inferred from polarized radio emission appears to be broadly consistent with that determined 6-8 years earlier. However, rotating vector model fits suggest that we are now seeing radio emission from a different location in the magnetosphere than previously. This indicates a novel way in which radio emission from magnetars can differ from that of ordinary pulsars. The torque on the neutron star is varying rapidly and unsteadily, as is common for magnetars following outburst, having changed by a factor of 7 within six months of reactivation.Comment: Published in ApJ (2018 April 5); 13 pages, 4 figure

Estimating the changing disease burden attributable to high body mass index for South Africa for 2000, 2006 and 2012

Background. A high body mass index (BMI) is associated with several cardiovascular diseases, diabetes and chronic kidney disease, cancers, and other selected health conditions. Objectives. To quantify the deaths and disability-adjusted life years (DALYs) attributed to high BMI in persons aged ≥20 years in South Africa (SA) for 2000, 2006 and 2012. Methods. The comparative risk assessment (CRA) methodology was followed. Meta-regressions of the BMI mean and standard deviation from nine national surveys spanning 1998 - 2017 were conducted to provide estimates by age and sex for adults aged ≥20 years. Population attributable fractions were calculated for selected health outcomes using relative risks identified by the Global Burden of Disease Study (2017), and applied to deaths and DALY estimates from the second South African National Burden of Disease Study to estimate the burden attributed to high BMI in a customised Microsoft Excel workbook. Monte Carlo simulation-modelling techniques were used for the uncertainty analysis. BMI was assumed to follow a log-normal distribution, and the theoretical minimum value of BMI below which no risk was estimated was assumed to follow a uniform distribution from 20 kg/m2 to 25 kg/m2. Results. Between 2000 and 2012, mean BMI increased by 6% from 27.7 kg/m2 (95% confidence interval (CI) 27.6 - 27.9) to 29.4 kg/m2 (95% CI 29.3 - 29.5) for females, and by 3% from 23.9 kg/m2 (95% CI 23.7 - 24.1) to 24.6 kg/m2 (95% CI 24.5 - 24.8) for males. In 2012, high BMI caused 58 757 deaths (95% uncertainty interval (UI) 46 740 - 67 590) or 11.1% (95% UI 8.8 - 12.8) of all deaths, and 1.42 million DALYs (95% UI 1.15 - 1.61) or 6.9% (95% UI 5.6 - 7.8) of all DALYs. Over the study period, the burden in females was ~1.5 - 1.8 times higher than that in males. Type 2 diabetes mellitus became the leading cause of death attributable to high BMI in 2012 (n=12 382 deaths), followed by hypertensive heart disease (n=12 146), haemorrhagic stroke (n=9 141), ischaemic heart disease (n=7 499) and ischaemic stroke (n=4 044). The age-standardised attributable DALY rate per 100 000 population for males increased by 6.6% from 3 777 (95% UI 2 639 - 4 869) in 2000 to 4 026 (95% UI 2 831 - 5 115) in 2012, while it increased by 7.8% for females from 6 042 (95% UI 5 064 - 6 702) to 6 513 (95% UI 5 597 - 7 033). Conclusion. Average BMI increased between 2000 and 2012 and accounted for a growing proportion of total deaths and DALYs. There is a need to develop, implement and evaluate comprehensive interventions to achieve lasting change in the determinants and impact of overweight and obesity, particularly among women