A portable platform for accelerated PIC codes and its application to GPUs using OpenACC

We present a portable platform, called PIC_ENGINE, for accelerating Particle-In-Cell (PIC) codes on heterogeneous many-core architectures such as Graphic Processing Units (GPUs). The aim of this development is efficient simulations on future exascale systems by allowing different parallelization strategies depending on the application problem and the specific architecture. To this end, this platform contains the basic steps of the PIC algorithm and has been designed as a test bed for different algorithmic options and data structures. Among the architectures that this engine can explore, particular attention is given here to systems equipped with GPUs. The study demonstrates that our portable PIC implementation based on the OpenACC programming model can achieve performance closely matching theoretical predictions. Using the Cray XC30 system, Piz Daint, at the Swiss National Supercomputing Centre (CSCS), we show that PIC_ENGINE running on an NVIDIA Kepler K20X GPU can outperform the one on an Intel Sandybridge 8-core CPU by a factor of 3.4

The in-plane electrodynamics of the superconductivity in Bi2Sr2CaCu2O8+d: energy scales and spectral weight distribution

The in-plane infrared and visible (3 meV-3 eV) reflectivity of Bi2Sr2CaCu2O8+d (Bi-2212) thin films is measured between 300 K and 10 K for different doping levels with unprecedented accuracy. The optical conductivity is derived through an accurate fitting procedure. We study the transfer of spectral weight from finite energy into the superfluid as the system becomes superconducting. In the over-doped regime, the superfluid develops at the expense of states lying below 60 meV, a conventional energy of the order of a few times the superconducting gap. In the underdoped regime, spectral weight is removed from up to 2 eV, far beyond any conventional scale. The intraband spectral weight change between the normal and superconducting state, if analyzed in terms of a change of kinetic energy is ~1 meV. Compared to the condensation energy, this figure addresses the issue of a kinetic energy driven mechanism.Comment: 13 pages with 9 figures include

Duplications of the critical Rubinstein-Taybi deletion region on chromosome 16p13.3 cause a novel recognisable syndrome

Background The introduction of molecular karyotyping technologies facilitated the identification of specific genetic disorders associated with imbalances of certain genomic regions. A detailed phenotypic delineation of interstitial 16p13.3 duplications is hampered by the scarcity of such patients. Objectives To delineate the phenotypic spectrum associated with interstitial 16p13.3 duplications, and perform a genotype-phenotype analysis. Results The present report describes the genotypic and phenotypic delineation of nine submicroscopic interstitial 16p13.3 duplications. The critically duplicated region encompasses a single gene, CREBBP, which is mutated or deleted in Rubinstein-Taybi syndrome. In 10 out of the 12 hitherto described probands, the duplication arose de novo. Conclusions Interstitial 16p13.3 duplications have a recognizable phenotype, characterized by normal to moderately retarded mental development, normal growth, mild arthrogryposis, frequently small and proximally implanted thumbs and characteristic facial features. Occasionally, developmental defects of the heart, genitalia, palate or the eyes are observed. The frequent de novo occurrence of 16p13.3 duplications demonstrates the reduced reproductive fitness associated with this genotype. Inheritance of the duplication from a clinically normal parent in two cases indicates that the associated phenotype is incompletely penetrant

ORB5: a global electromagnetic gyrokinetic code using the PIC approach in toroidal geometry

This paper presents the current state of the global gyrokinetic code ORB5 as an update of the previous reference [Jolliet et al., Comp. Phys. Commun. 177 409 (2007)]. The ORB5 code solves the electromagnetic Vlasov-Maxwell system of equations using a PIC scheme and also includes collisions and strong flows. The code assumes multiple gyrokinetic ion species at all wavelengths for the polarization density and drift-kinetic electrons. Variants of the physical model can be selected for electrons such as assuming an adiabatic response or a ``hybrid'' model in which passing electrons are assumed adiabatic and trapped electrons are drift-kinetic. A Fourier filter as well as various control variates and noise reduction techniques enable simulations with good signal-to-noise ratios at a limited numerical cost. They are completed with different momentum and zonal flow-conserving heat sources allowing for temperature-gradient and flux-driven simulations. The code, which runs on both CPUs and GPUs, is well benchmarked against other similar codes and analytical predictions, and shows good scalability up to thousands of nodes

Linearized model Fokker-Planck collision operators for gyrokinetic simulations. II. Numerical implementation and tests

A set of key properties for an ideal dissipation scheme in gyrokinetic simulations is proposed, and implementation of a model collision operator satisfying these properties is described. This operator is based on the exact linearized test-particle collision operator, with approximations to the field-particle terms that preserve conservation laws and an H-Theorem. It includes energy diffusion, pitch-angle scattering, and finite Larmor radius effects corresponding to classical (real-space) diffusion. The numerical implementation in the continuum gyrokinetic code GS2 is fully implicit and guarantees exact satisfaction of conservation properties. Numerical results are presented showing that the correct physics is captured over the entire range of collisionalities, from the collisionless to the strongly collisional regimes, without recourse to artificial dissipation.Comment: 13 pages, 8 figures, submitted to Physics of Plasmas; typos fixe

Remote sensing and geographic information systems: charting Sin Nombre virus infections in deer mice.

We tested environmental data from remote sensing and geographic information system maps as indicators of Sin Nombre virus (SNV) infections in deer mouse (Peromyscus maniculatus) populations in the Walker River Basin, Nevada and California. We determined by serologic testing the presence of SNV infections in deer mice from 144 field sites. We used remote sensing and geographic information systems data to characterize the vegetation type and density, elevation, slope, and hydrologic features of each site. The data retroactively predicted infection status of deer mice with up to 80% accuracy. If models of SNV temporal dynamics can be integrated with baseline spatial models, human risk for infection may be assessed with reasonable accuracy

Combined potential and spin impurity scattering in cuprates

We present a theory of combined nonmagnetic and magnetic impurity scattering in anisotropic superconductors accounting for the momentum-dependent impurity potential. Applying the model to the d-wave superconducting state, we obtain a quantitative agreement with the initial suppression of the critical temperature due to Zn and Ni substitutions as well as electron irradiation defects in the cuprates. We suggest, that the unequal pair-breaking effect of Zn and Ni may be related to a different nature of the magnetic moments induced by these impurities.Comment: 5 pages, 3 tables, RevTex, to be published in Phys. Rev.

Nonlinear interaction of Alfv\'enic instabilities and turbulence via the modification of the equilibrium profiles

Nonlinear simulations of Alfv\'en modes (AM) driven by energetic particles (EP) in the presence of turbulence are performed with the gyrokinetic particle-in-cell code ORB5. The AMs carry a heat flux, and consequently they nonlinearly modify the plasma temperature profiles. The isolated effect of this modification on the dynamics of turbulence is studied, by means of electrostatic simulations. We find that turbulence is reduced when the profiles relaxed by the AM are used, with respect to the simulation where the unperturbed profiles are used. This is an example of indirect interaction of EPs and turbulence. First, an analytic magnetic equilibrium with circular concentric flux surfaces is considered as a simplified example for this study. Then, an application to an experimentally relevant case of ASDEX Upgrade is discussed

Virtual reality, ultrasound-guided liver biopsy simulator: Development and performance discrimination

Objectives: The aim of this article was to identify and prospectively investigate simulated ultrasound-guided targeted liver biopsy performance metrics as differentiators between levels of expertise in interventional radiology. Methods: Task analysis produced detailed procedural step documentation allowing identification of critical procedure steps and performance metrics for use in a virtual reality ultrasound-guided targeted liver biopsy procedure. Consultant (n=14; male=11, female=3) and trainee (n=26; male=19, female=7) scores on the performance metrics were compared. Ethical approval was granted by the Liverpool Research Ethics Committee (UK). Independent t-tests and analysis of variance (ANOVA) investigated differences between groups. Results: Independent t-tests revealed significant differences between trainees and consultants on three performance metrics: targeting, p=0.018, t=22.487 (22.040 to 20.207); probe usage time, p=0.040, t=2.132 (11.064 to 427.983); mean needle length in beam, p=0.029, t=22.272 (20.028 to 20.002). ANOVA reported significant differences across years of experience (0–1, 1–2, 3+ years) on seven performance metrics: no-go area touched, p=0.012; targeting, p=0.025; length of session, p=0.024; probe usage time, p=0.025; total needle distance moved, p=0.038; number of skin contacts, p<0.001; total time in no-go area, p=0.008. More experienced participants consistently received better performance scores on all 19 performance metrics. Conclusion: It is possible to measure and monitor performance using simulation, with performance metrics providing feedback on skill level and differentiating levels of expertise. However, a transfer of training study is required