Gyrokinetic particle-in-cell optimization on emerging multi- and manycore platforms

The next decade of high-performance computing (HPC) systems will see a rapid evolution and divergence of multi- and manycore architectures as power and cooling constraints limit increases in microprocessor clock speeds. Understanding efficient optimization methodologies on diverse multicore designs in the context of demanding numerical methods is one of the greatest challenges faced today by the HPC community. In this work, we examine the efficient multicore optimization of GTC, a petascale gyrokinetic toroidal fusion code for studying plasma microturbulence in tokamak devices. For GTC’s key computational components (charge deposition and particle push), we explore efficient parallelization strategies across a broad range of emerging multicore designs, including the recently-released Intel Nehalem-EX, the AMD Opteron Istanbul, and the highly multithreaded Sun UltraSparc T2+. We also present the first study on tuning gyrokinetic particle-in-cell (PIC) algorithms for graphics processors, using the NVIDIA C2050 (Fermi). Our work discusses several novel optimization approaches for gyrokinetic PIC, including mixed-precision computation, particle binning and decomposition strategies, grid replication, SIMDized atomic floating-point operations, and effective GPU texture memory utilization. Overall, we achieve significant performance improvements of 1.3-4.7× on these complex PIC kernels, despite the inherent challenges of data dependency and locality. Our work also points to several architectural and programming features that could significantly enhance PIC performance and productivity on next-generation architectures.     

Laser ablation in a model two-phase system

Short pulse laser ablation of a model two-component system has been simulated using a coarse-grained molecular dynamics (MD) model. A system with two disparate components (hard and soft) has been considered, based broadly on the properties of hard tissue. The existence of distinct regimes of material ejection has been identified and the processes leading to the ablation have been investigated. In the lower fluence regime gaseous particles of the soft component stream from the hard matrix but there is no ejection of the hard component. In the higher fluence regime chunks of the hard component are ejected simultaneously with the soft component.     

ITER safety and licensing update

Safety files were submitted by the ITER Organization to the French nuclear safety authorities in March 2010 as a part of the licensing process. These included the preliminary safety report (RPrS) which presents the extensive safety analyses performed for ITER. The report has been the subject of examination by the authorities and their advisors, and discussions with them have been held on many topics. In the light of this process, this paper discusses some of the topics that remain prominent in the safety analysis of ITER. In particular, the provision of the two safety functions, confinement of radioactive material and limitation of exposure to radiation, is explained and some of the potential challenges to them are identified. Amongst these are the risks of fire and explosion, and external events such as earthquake and loss of all electric power. Provisions in the ITER design, together with the characteristics of fusion, ensure that a very good safety performance will be achieved.     

Oxidation of titanium carbide–graphite hetero-modulus ceramics with low carbon content: II. Physico-chemical interpretation of the ridge effect

Hetero-modulus ceramics (HMC) present the combination of a ceramic matrix with the inclusions of a dispersed phase with considerably lower Young's modulus, resulting in a material with significantly improved properties. An interpretation of the so-called “ridge effect” observed during the isobaric-isothermal oxidation of 93 vol% TiC–7 vol% C (graphite) HMC at temperatures of 400–1000 °C and oxygen pressures of 0.13–65 kPa is given. Established in Part I of this study, the meanings of a ridge temperature and ridge oxygen pressure, which are served as boundaries between prevailing oxidation mechanisms in phenomenological kinetics model, are considered on the basis of X-ray diffraction (XRD) and microscopy analyses. The oxidation mechanisms, essentially different within the studied ranges of temperatures and oxygen pressures are identified according to the developed general model. These results can be used for the preparation of special protective coatings on the surface of refractory carbide–carbon HMC parts applied in severe environments, e.g. chemically active, high-enthalpy gaseous flows.     

The properties of nanocomposite coatings formed on a steel 20H surface by means of electrospark processing using rod-shaped electrodes of steels 65 G and Sv 08

The phase composition, the sizes of the grains (crystallites), the microstructure and microhardness, and the physical and mechanical properties of the nanocomposite coatings on the 20H steel surface resulting from the electrical processing in a gas medium by compact electrodes made of steels 65G and Sv08 with regard to the processing velocity and their influence on the wear resistance of the composition have been investigated.     

Determining the internal friction coefficient for gland packing

A method is proposed for determining the internal-friction coefficient f_i.f of gland packing based on thermally expanded graphite (TEG). The f_i.f calculations are based on experimental data for packing of three types: N1100, N1201, and N5001. __________ Translated from Khimicheskoe i Neftegazovoe Mashinostroenie, No. 7, pp. 43–44, July, 2007.     

Changes in the Cardiotoxic Effects of Lead Intoxication in Rats Induced by Muscular Exercise

Exposure to lead is associated with an increased risk of cardiovascular diseases. Outbred white male rats were injected with lead acetate intraperitoneally three times a week and/or were forced to run at a speed of 25 m/min for 10 min 5 days a week. We performed noninvasive recording of arterial pressure, electrocardiogram and breathing parameters, and assessed some biochemical characteristics. Electrophoresis in polyacrylamide gel was used to determine the ratio of myosin heavy chains. An in vitro motility assay was employed to measure the sliding velocity of regulated thin filaments on myosin. Isolated multicellular preparations of the right ventricle myocardium were used to study contractility in isometric and physiological modes of contraction. Exercise under lead intoxication normalized the level of calcium and activity of the angiotensin-converting enzyme in the blood serum, normalized the isoelectric line voltage and T-wave amplitude on the electrocardiogram, increased the level of creatine kinase-MB and reduced the inspiratory rate. Additionally, the maximum sliding velocity and the myosin heavy chain ratio were partly normalized. The effect of exercise under lead intoxication on myocardial contractility was found to be variable. In toto, muscular loading was found to attenuate the effects of lead intoxication, as judged by the indicators of the cardiovascular system.     

Isolated Variable Domains of an Antibody Can Assemble on Blood Coagulation Factor VIII into a Functional Fv-like Complex

Single-chain variable fragments (scFv) are antigen-recognizing variable fragments of antibodies (FV) where both subunits (V_L and V_H) are connected via an artificial linker. One particular scFv, iKM33, directed against blood coagulation factor VIII (FVIII) was shown to inhibit major FVIII functions and is useful in FVIII research. We aimed to investigate the properties of iKM33 enabled with protease-dependent disintegration. Three variants of iKM33 bearing thrombin cleavage sites within the linker were expressed using a baculovirus system and purified by two-step chromatography. All proteins retained strong binding to FVIII by surface plasmon resonance, and upon thrombin cleavage, dissociated into V_L and V_H as shown by size-exclusion chromatography. However, in FVIII activity and low-density lipoprotein receptor-related protein 1 binding assays, the thrombin-cleaved iKM33 variants were still inhibitory. In a pull-down assay using an FVIII-affinity sorbent, the isolated V_H, a mixture of V_L and V_H, and intact iKM33 were carried over via FVIII analyzed by electrophoresis. We concluded that the isolated V_L and V_H assembled into scFv-like heterodimer on FVIII, and the isolated V_H alone also bound FVIII. We discuss the potential use of both protease-cleavable scFvs and isolated Fv subunits retaining high affinity to the antigens in various practical applications such as therapeutics, diagnostics, and research.