Automatic Loop Kernel Analysis and Performance Modeling With Kerncraft

Analytic performance models are essential for understanding the performance characteristics of loop kernels, which consume a major part of CPU cycles in computational science. Starting from a validated performance model one can infer the relevant hardware bottlenecks and promising optimization opportunities. Unfortunately, analytic performance modeling is often tedious even for experienced developers since it requires in-depth knowledge about the hardware and how it interacts with the software. We present the "Kerncraft" tool, which eases the construction of analytic performance models for streaming kernels and stencil loop nests. Starting from the loop source code, the problem size, and a description of the underlying hardware, Kerncraft can ideally predict the single-core performance and scaling behavior of loops on multicore processors using the Roofline or the Execution-Cache-Memory (ECM) model. We describe the operating principles of Kerncraft with its capabilities and limitations, and we show how it may be used to quickly gain insights by accelerated analytic modeling.Comment: 11 pages, 4 figures, 8 listing

Automatic Throughput and Critical Path Analysis of x86 and ARM Assembly Kernels

Useful models of loop kernel runtimes on out-of-order architectures require an analysis of the in-core performance behavior of instructions and their dependencies. While an instruction throughput prediction sets a lower bound to the kernel runtime, the critical path defines an upper bound. Such predictions are an essential part of analytic (i.e., white-box) performance models like the Roofline and Execution-Cache-Memory (ECM) models. They enable a better understanding of the performance-relevant interactions between hardware architecture and loop code. The Open Source Architecture Code Analyzer (OSACA) is a static analysis tool for predicting the execution time of sequential loops. It previously supported only x86 (Intel and AMD) architectures and simple, optimistic full-throughput execution. We have heavily extended OSACA to support ARM instructions and critical path prediction including the detection of loop-carried dependencies, which turns it into a versatile cross-architecture modeling tool. We show runtime predictions for code on Intel Cascade Lake, AMD Zen, and Marvell ThunderX2 micro-architectures based on machine models from available documentation and semi-automatic benchmarking. The predictions are compared with actual measurements.Comment: 6 pages, 3 figure

Automated Instruction Stream Throughput Prediction for Intel and AMD Microarchitectures

An accurate prediction of scheduling and execution of instruction streams is a necessary prerequisite for predicting the in-core performance behavior of throughput-bound loop kernels on out-of-order processor architectures. Such predictions are an indispensable component of analytical performance models, such as the Roofline and the Execution-Cache-Memory (ECM) model, and allow a deep understanding of the performance-relevant interactions between hardware architecture and loop code. We present the Open Source Architecture Code Analyzer (OSACA), a static analysis tool for predicting the execution time of sequential loops comprising x86 instructions under the assumption of an infinite first-level cache and perfect out-of-order scheduling. We show the process of building a machine model from available documentation and semi-automatic benchmarking, and carry it out for the latest Intel Skylake and AMD Zen micro-architectures. To validate the constructed models, we apply them to several assembly kernels and compare runtime predictions with actual measurements. Finally we give an outlook on how the method may be generalized to new architectures.Comment: 11 pages, 4 figures, 7 table

Deceleration of neutral molecules in macroscopic traveling traps

A new type of decelerator is presented where polar neutral molecules are guided and decelerated using the principle of traveling electric potential wells, such that molecules are confined in stable three-dimensional traps throughout. This new decelerator is superior to the best currently operational decelerator (Scharfenberg et al., Phys.Rev.A 79, 023410(2009)), providing a substantially larger acceptance even at higher accelerations. The mode of operation is described and experimentally demonstrated by guiding and decelerating CO molecules.Comment: 10 pages, 3 figure

Effect of Experimental Thyrotoxicosis onto Blood Coagulation: A Proteomics Study

Background: Hyperthyroidism is known to induce a hypercoagulable state. It stimulates plasma levels of procoagulative factors and reduces fibrinolytic activity. So far most of the data have been derived from patients with endogenous hyperthyroidism with a wide variability in the underlying pathogenesis and severity of the disease. Objectives: In this study we experimentally induced thyrotoxicosis in healthy volunteers to explore the effects of thyroxine excess on the plasma proteome. Using a shotgun proteomics approach, the abundance of plasma proteins was monitored before, during and after thyrotoxicosis. Methods: Sixteen healthy male subjects were sampled at baseline, 4 and 8 weeks under 250 µg/day thyroxine p.o., as well as 4 and 8 weeks after stopping the application. Plasma proteins were analyzed after depletion of 6 high-abundance proteins (MARS6) by LC-ESI-MS/MS mass spectrometry. Mass spectrometric raw data were processed using a label-free, intensity-based workflow. Subsequently, the linear dependence between protein abundances and fT4 levels were calculated using a Pearson correlation. Results: All subjects developed biochemical thyrotoxicosis, and this effect was reversed within the first 4 weeks of follow-up. None of the volunteers noticed any subjective symptoms. Levels of 10 proteins involved in the coagulation cascade specifically correlated with fT4, supporting an influence of thyroid hormone levels on blood coagulation even at nonpathological levels. Conclusions: The results suggest that experimental thyrotoxicosis exerts selective and specific thyroxine-induced effects on coagulation markers. Our study design allows assessment of thyroid hormone effects on plasma protein levels without secondary effects of other diseases or therapies

Reply to the comment on "Imaging of the Hydrogen Subsurface Site in Rutile TiO2''

A reply to the Comment by M. Calatayud et al. on "Imaging of the Hydrogen Subsurface Site in Rutile TiO2" (Physical Review Letters, Volume 102, Issue 13). DOI: 10.1103/physrevlett.102.136103.Peer reviewe

Plasma proteome and metabolome characterization of an experimental human thyrotoxicosis model.

BACKGROUND: Determinations of thyrotropin (TSH) and free thyroxine (FT4) represent the gold standard in evaluation of thyroid function. To screen for novel peripheral biomarkers of thyroid function and to characterize FT4-associated physiological signatures in human plasma we used an untargeted OMICS approach in a thyrotoxicosis model. METHODS: A sample of 16 healthy young men were treated with levothyroxine for 8 weeks and plasma was sampled before the intake was started as well as at two points during treatment and after its completion, respectively. Mass spectrometry-derived metabolite and protein levels were related to FT4 serum concentrations using mixed-effect linear regression models in a robust setting. To compile a molecular signature discriminating between thyrotoxicosis and euthyroidism, a random forest was trained and validated in a two-stage cross-validation procedure. RESULTS: Despite the absence of obvious clinical symptoms, mass spectrometry analyses detected 65 metabolites and 63 proteins exhibiting significant associations with serum FT4. A subset of 15 molecules allowed a robust and good prediction of thyroid hormone function (AUC = 0.86) without prior information on TSH or FT4. Main FT4-associated signatures indicated increased resting energy expenditure, augmented defense against systemic oxidative stress, decreased lipoprotein particle levels, and increased levels of complement system proteins and coagulation factors. Further association findings question the reliability of kidney function assessment under hyperthyroid conditions and suggest a link between hyperthyroidism and cardiovascular diseases via increased dimethylarginine levels. CONCLUSION: Our results emphasize the power of untargeted OMICs approaches to detect novel pathways of thyroid hormone action. Furthermore, beyond TSH and FT4, we demonstrated the potential of such analyses to identify new molecular signatures for diagnosis and treatment of thyroid disorders. This study was registered at the German Clinical Trials Register (DRKS) [DRKS00011275] on the 16th of November 2016

Imaging of the Hydrogen Subsurface Site in Rutile TiO2

From an interplay between simultaneously recorded noncontact atomic force microscopy and scanning tunneling microscopy images and simulations based on density functional theory, we reveal the location of single hydrogen species in the surface and subsurface layers of rutile TiO2. Subsurface hydrogen atoms (Hsub) are found to reside in a stable interstitial site as subsurface OH groups detectable in scanning tunneling microscopy as a characteristic electronic state but imperceptible to atomic force microscopy. The combined atomic force microscopy, scanning tunneling microscopy, and density functional theory study demonstrates a general scheme to reveal near surface defects and interstitials in poorly conducting materials.Peer reviewe

Prenatal Exposure to Perfluorooctanoate and Risk of Overweight at 20 Years of Age: A Prospective Cohort Study

Background: Perfluoroalkyl acids are persistent compounds used in various industrial -applications. Of these compounds, perfluorooctanoate (PFOA) is currently detected in humans worldwide. A recent study on low-dose developmental exposure to PFOA in mice reported increased weight and elevated biomarkers of adiposity in postpubertal female offspring