An efficient and portable SIMD algorithm for charge/current deposition in Particle-In-Cell codes

In current computer architectures, data movement (from die to network) is by far the most energy consuming part of an algorithm (10pJ/word on-die to 10,000pJ/word on the network). To increase memory locality at the hardware level and reduce energy consumption related to data movement, future exascale computers tend to use more and more cores on each compute nodes ("fat nodes") that will have a reduced clock speed to allow for efficient cooling. To compensate for frequency decrease, machine vendors are making use of long SIMD instruction registers that are able to process multiple data with one arithmetic operator in one clock cycle. SIMD register length is expected to double every four years. As a consequence, Particle-In-Cell (PIC) codes will have to achieve good vectorization to fully take advantage of these upcoming architectures. In this paper, we present a new algorithm that allows for efficient and portable SIMD vectorization of current/charge deposition routines that are, along with the field gathering routines, among the most time consuming parts of the PIC algorithm. Our new algorithm uses a particular data structure that takes into account memory alignement constraints and avoids gather/scatter instructions that can significantly affect vectorization performances on current CPUs. The new algorithm was successfully implemented in the 3D skeleton PIC code PICSAR and tested on Haswell Xeon processors (AVX2-256 bits wide data registers). Results show a factor of $\times 2$ to $\times 2.5$ speed-up in double precision for particle shape factor of order $1$ to $3$. The new algorithm can be applied as is on future KNL (Knights Landing) architectures that will include AVX-512 instruction sets with 512 bits register lengths (8 doubles/16 singles).Comment: 36 pages, 5 figure

Correlated defects, metal-insulator transition, and magnetic order in ferromagnetic semiconductors

The effect of disorder on transport and magnetization in ferromagnetic III-V semiconductors, in particular (Ga,Mn)As, is studied theoretically. We show that Coulomb-induced correlations of the defect positions are crucial for the transport and magnetic properties of these highly compensated materials. We employ Monte Carlo simulations to obtain the correlated defect distributions. Exact diagonalization gives reasonable results for the spectrum of valence-band holes and the metal-insulator transition only for correlated disorder. Finally, we show that the mean-field magnetization also depends crucially on defect correlations.Comment: 4 pages RevTeX4, 5 figures include

Untargeted metabolomic profile for the detection of prostate carcinoma-preliminary results from PARAFAC2 and PLS-DA Models

Prostate-specific antigen (PSA) is the main biomarker for the screening of prostate cancer (PCa), which has a high sensibility (higher than 80%) that is negatively offset by its poor specificity (only 30%, with the European cut-off of 4 ng/mL). This generates a large number of useless biopsies, involving both risks for the patients and costs for the national healthcare systems. Consequently, efforts were recently made to discover new biomarkers useful for PCa screening, including our proposal of interpreting a multi-parametric urinary steroidal profile with multivariate statistics. This approach has been expanded to investigate new alleged biomarkers by the application of untargeted urinary metabolomics. Urine samples from 91 patients (43 affected by PCa; 48 by benign hyperplasia) were deconjugated, extracted in both basic and acidic conditions, derivatized with different reagents, and analyzed with different gas chromatographic columns. Three-dimensional data were obtained from full-scan electron impact mass spectra. The PARADISe software, coupled with NIST libraries, was employed for the computation of PARAFAC2 models, the extraction of the significative components (alleged biomarkers), and the generation of a semiquantitative dataset. After variables selection, a partial least squares–discriminant analysis classification model was built, yielding promising performances. The selected biomarkers need further validation, possibly involving, yet again, a targeted approach

Shaping concepts of technology : what concepts and how to shape them?

Philosophy of technology is a discipline that has much to offer for technology education. Insights into the real nature of technology and its relationship with science and society can help technology educators to build a subject that helps pupils get a good concept of technology and to learn to understand and use concepts in technology. Here the way science educators have gained from the philosophy of science, for example in the idea of the way pupils learn concepts by reconstructing pre-concepts that they picked up from daily-life experiences. Research has shown that the learning of concepts and the learning of process skills have to be connected

Sharp interface limits of phase-field models

The use of continuum phase-field models to describe the motion of well-defined interfaces is discussed for a class of phenomena, that includes order/disorder transitions, spinodal decomposition and Ostwald ripening, dendritic growth, and the solidification of eutectic alloys. The projection operator method is used to extract the ``sharp interface limit'' from phase field models which have interfaces that are diffuse on a length scale $\xi$. In particular,phase-field equations are mapped onto sharp interface equations in the limits $\xi \kappa \ll 1$ and $\xi v/D \ll 1$, where $\kappa$ and $v$ are respectively the interface curvature and velocity and $D$ is the diffusion constant in the bulk. The calculations provide one general set of sharp interface equations that incorporate the Gibbs-Thomson condition, the Allen-Cahn equation and the Kardar-Parisi-Zhang equation.Comment: 17 pages, 9 figure