Energy aware approach for HPC systems

International audienceHigh‐performance computing (HPC) systems require energy during their full life cycle from design and production to transportation to usage and recycling/dismanteling. Because of increase of ecological and cost awareness, energy performance is now a primary focus. This chapter focuses on the usage aspect of HPC and how adapted and optimized software solutions could improve energy efficiency. It provides a detailed explanation of server power consumption, and discusses the application of HPC, phase detection, and phase identification. The chapter also suggests that having the load and memory access profiles is insufficient for an effective evaluation of the power consumed by an application. The available leverages in HPC systems are also shown in detail. The chapter proposes some solutions for modeling the power consumption of servers, which allows designing power prediction models for better decision making.These approaches allow the deployment and usage of a set of available green leverages, permitting energy reduction

CSS100603:112253-111037: A helium-rich dwarf nova with a 65 minute orbital period

We present time-resolved optical spectroscopy of the dwarf nova CSS100603:112253-111037. Its optical spectrum is rich in helium, with broad, double-peaked emission lines produced in an accretion disc. We measure a line flux ratio HeI5876/H_alpha = 1.49 +/- 0.04, a much higher ratio than is typically observed in dwarf novae. The orbital period, as derived from the radial velocity of the line wings, is 65.233 +/- 0.015 minutes. In combination with the previously measured superhump period, this implies an extreme mass ratio of M_2/M_1 = 0.017 +/- 0.004. The H_alpha and HeI6678 emission lines additionally have a narrow central spike, as is often seen in the spectra of AM CVn type stars. Comparing its properties with CVs, AM CVn systems and hydrogen binaries below the CV period minimum, we argue that CSS100603:112253-111037 is the first compelling example of an AM CVn system forming via the evolved CV channel. With the addition of this system, evolved cataclysmic variables (CVs) now account for seven per cent of all known semi-detached white dwarf binaries with Porb < 76 min. Two recently discovered binaries may further increase this figure. Although the selection bias of this sample is not yet well defined, these systems support the evolved CV model as a possible formation channel for ultracompact accreting binaries. The orbital periods of the three ultracompact hydrogen accreting binaries overlap with those of the long period AM CVn stars, but there are currently no known systems in the period range 67 - 76 minutes.Comment: 10 pages, 6 figures. Accepted for publication in MNRA

The Effect of Lattice Vibrations on Substitutional Alloy Thermodynamics

A longstanding limitation of first-principles calculations of substitutional alloy phase diagrams is the difficulty to account for lattice vibrations. A survey of the theoretical and experimental literature seeking to quantify the impact of lattice vibrations on phase stability indicates that this effect can be substantial. Typical vibrational entropy differences between phases are of the order of 0.1 to 0.2 k_B/atom, which is comparable to the typical values of configurational entropy differences in binary alloys (at most 0.693 k_B/atom). This paper describes the basic formalism underlying ab initio phase diagram calculations, along with the generalization required to account for lattice vibrations. We overview the various techniques allowing the theoretical calculation and the experimental determination of phonon dispersion curves and related thermodynamic quantities, such as vibrational entropy or free energy. A clear picture of the origin of vibrational entropy differences between phases in an alloy system is presented that goes beyond the traditional bond counting and volume change arguments. Vibrational entropy change can be attributed to the changes in chemical bond stiffness associated with the changes in bond length that take place during a phase transformation. This so-called ``bond stiffness vs. bond length'' interpretation both summarizes the key phenomenon driving vibrational entropy changes and provides a practical tool to model them.Comment: Submitted to Reviews of Modern Physics 44 pages, 6 figure

Resonant Auger spectroscopy at the L2,3 shake-up thresholds as a probe of electron correlation effects in nickel

The excitation energy dependence of the three-hole satellites in the L3-M4,5M4,5 and L2-M4,5M4,5 Auger spectra of nickel metal has been measured using synchrotron radiation. The satellite behavior in the non-radiative emission spectra at the L3 and L2 thresholds is compared and the influence of the Coster-Kronig channel explored. The three-hole satellite intensity at the L3 Auger emission line reveals a peak structure at 5 eV above the L3 threshold attributed to resonant processes at the 2p53d9 shake-up threshold. This is discussed in connection with the 6-eV feature in the x-ray absorption spectrum.Comment: 8 pages, 4 figures; http://prb.aps.org/abstract/PRB/v58/i7/p3677_

Opto-Current-Clamp Actuation of Cortical Neurons Using a Strategically Designed Channelrhodopsin

BACKGROUND: Optogenetic manipulation of a neuronal network enables one to reveal how high-order functions emerge in the central nervous system. One of the Chlamydomonas rhodopsins, channelrhodopsin-1 (ChR1), has several advantages over channelrhodopsin-2 (ChR2) in terms of the photocurrent kinetics. Improved temporal resolution would be expected by the optogenetics using the ChR1 variants with enhanced photocurrents. METHODOLOGY/PRINCIPAL FINDINGS: The photocurrent retardation of ChR1 was overcome by exchanging the sixth helix domain with its counterpart in ChR2 producing Channelrhodopsin-green receiver (ChRGR) with further reform of the molecule. When the ChRGR photocurrent was measured from the expressing HEK293 cells under whole-cell patch clamp, it was preferentially activated by green light and has fast kinetics with minimal desensitization. With its kinetic advantages the use of ChRGR would enable one to inject a current into a neuron by the time course as predicted by the intensity of the shedding light (opto-current clamp). The ChRGR was also expressed in the motor cortical neurons of a mouse using Sindbis pseudovirion vectors. When an oscillatory LED light signal was applied sweeping through frequencies, it robustly evoked action potentials synchronized to the oscillatory light at 5-10 Hz in layer 5 pyramidal cells in the cortical slice. The ChRGR-expressing neurons were also driven in vivo with monitoring local field potentials (LFPs) and the time-frequency energy distribution of the light-evoked response was investigated using wavelet analysis. The oscillatory light enhanced both the in-phase and out-phase responses of LFP at the preferential frequencies of 5-10 Hz. The spread of activity was evidenced by the fact that there were many c-Fos-immunoreactive neurons that were negative for ChRGR in a region of the motor cortex. CONCLUSIONS/SIGNIFICANCE: The opto-current-clamp study suggests that the depolarization of a small number of neurons wakes up the motor cortical network over some critical point to the activated state

Highly sensitive and rapid determination of tacrolimus in peripheral blood mononuclear cells by liquid chromatography–tandem mass spectrometry

After solid organ transplantation, tacrolimus is given to prevent rejection. Therapeutic drug monitoring is used to reach target concentrations of tacrolimus in whole blood. Because the site of action of tacrolimus is the lymphocyte, and tacrolimus binds ~80% to erythrocytes, the intracellular tacrolimus concentration in lymphocytes is possibly more relevant. For this purpose, we aimed to develop, improve and validate a UPLC–MS/MS method to measure tacrolimus concentrations in isolated peripheral blood mononuclear cells (PBMCs). PBMCs were isolated using a Ficoll separation technique, followed by a washing step using red blood cell lysis. A cell suspension of 50 μL containing 1 million PBMCs was used in combination with MagSiMUS-TDMPREP. To each sample we added 30 μL lysis buffer, 20 μL reconstitution buffer containing 13C2H4-tacrolimus as internal standard, 40 μL MagSiMUS-TDMPREP Type I Particle Mix and 175 μL Organic Precipitation Reagent VI for methanol-based protein precipitation. A 10 μL aliquot of the supernatant was injected into the UPLC–MS/MS system. The method was validated, resulting in high sensitivity and specificity. The method was linear (r2 = 0.997) over the range 5.0–1250 pg/1 × 106 PBMCs. The inaccuracy was <5% and the imprecision was <15%. The washing steps following Ficoll isolation could be performed at either room temperature or on ice, with no effect of the temperature on the results. A method for the analysis of tacrolimus concentrations in PBMCs was developed and successfully validated. Further research will be performed to investigate the correlation between concentrations in PBMCs and clinical outcome

Survival of non-Western first generations immigrants with stomach cancer in North East Netherlands

Background: Isolated groups, such as first generation non-Western immigrants, are at risk for suboptimal utilisation of the health care system resulting in a worse outcome. Methods: From 1989 to 2007, all patients with stomach cancer were selected from the Comprehensive Cancer Centre North-East cancer registry. Associations between country of birth and patient, tumour and treatment characteristics were determined using χ2 analysis. Relative survival analysis was used to estimate relative excess risk of dying according to country of birth (non-Western vs Western). Results: After adjusting for confounding factors (patient, tumour and treatment related), the risk of dying was lower for first generation non-Western immigrants (relative excess risk 0.55, 95% confidence interval 0.43–0.70) compared with Western patients. Conclusion: Although the better survival of first generation non-Western immigrants with stomach cancer remains unexplained, it argues against accessibility problems within the Dutch health care syste

Instagrammatics and digital methods: Studying visual social media, from selfies and GIFs to memes and emoji

Visual content is a critical component of everyday social media, on platforms explicitly framed around the visual (Instagram and Vine), on those offering a mix of text and images in myriad forms (Facebook, Twitter, and Tumblr), and in apps and profiles where visual presentation and provision of information are important considerations. However, despite being so prominent in forms such as selfies, looping media, infographics, memes, online videos, and more, sociocultural research into the visual as a central component of online communication has lagged behind the analysis of popular, predominantly text-driven social media. This paper underlines the increasing importance of visual elements to digital, social, and mobile media within everyday life, addressing the significant research gap in methods for tracking, analysing, and understanding visual social media as both image-based and intertextual content.In this paper, we build on our previous methodological considerations of Instagram in isolation to examine further questions, challenges, and benefits of studying visual social media more broadly, including methodological and ethical considerations. Our discussion is intended as a rallying cry and provocation for further research into visual (and textual and mixed) social media content, practices, and cultures, mindful of both the specificities of each form, but also, and importantly, the ongoing dialogues and interrelations between them as communication forms