Semi-automatic assessment of I/O behavior by inspecting the individual client-node timelines— an explorative study on 10^6 jobs

HPC applications with suboptimal I/O behavior interfere with well-behaving applications and lead to increased application runtime. In some cases, this may even lead to unresponsive systems and unfinished jobs. HPC monitoring systems can aid users and support staff to identify problematic behavior and support optimization of problematic applications. The key issue is how to identify relevant applications? A profile of an application doesn’t allow to identify problematic phases during the execution but tracing of each individual I/O is too invasive. In this work, we split the execution into segments, i.e., windows of fixed size and analyze profiles of them. We develop three I/O metrics to identify three relevant classes of inefficient I/O behaviors, and evaluate them on raw data of 1,000,000 jobs on the supercomputer Mistral. The advantages of our method is that temporal information about I/O activities during job runtime is preserved to some extent and can be used to identify phases of inefficient I/O. The main contribution of this work is the segmentation of time series and computation of metrics (Job-I/O-Utilization, Job-I/O-Problem-Time, and Job-I/O-Balance) that are effective to identify problematic I/O phases and jobs

Continuous, Semi-discrete, and Fully Discretized Navier-Stokes Equations

The Navier--Stokes equations are commonly used to model and to simulate flow phenomena. We introduce the basic equations and discuss the standard methods for the spatial and temporal discretization. We analyse the semi-discrete equations -- a semi-explicit nonlinear DAE -- in terms of the strangeness index and quantify the numerical difficulties in the fully discrete schemes, that are induced by the strangeness of the system. By analyzing the Kronecker index of the difference-algebraic equations, that represent commonly and successfully used time stepping schemes for the Navier--Stokes equations, we show that those time-integration schemes factually remove the strangeness. The theoretical considerations are backed and illustrated by numerical examples.Comment: 28 pages, 2 figure, code available under DOI: 10.5281/zenodo.998909, https://doi.org/10.5281/zenodo.99890

Artifact Rejection Methodology Enables Continuous, Noninvasive Measurement of Gastric Myoelectric Activity in Ambulatory Subjects.

The increasing prevalence of functional and motility gastrointestinal (GI) disorders is at odds with bottlenecks in their diagnosis, treatment, and follow-up. Lack of noninvasive approaches means that only specialized centers can perform objective assessment procedures. Abnormal GI muscular activity, which is coordinated by electrical slow-waves, may play a key role in symptoms. As such, the electrogastrogram (EGG), a noninvasive means to continuously monitor gastric electrical activity, can be used to inform diagnoses over broader populations. However, it is seldom used due to technical issues: inconsistent results from single-channel measurements and signal artifacts that make interpretation difficult and limit prolonged monitoring. Here, we overcome these limitations with a wearable multi-channel system and artifact removal signal processing methods. Our approach yields an increase of 0.56 in the mean correlation coefficient between EGG and the clinical "gold standard", gastric manometry, across 11 subjects (p < 0.001). We also demonstrate this system's usage for ambulatory monitoring, which reveals myoelectric dynamics in response to meals akin to gastric emptying patterns and circadian-related oscillations. Our approach is noninvasive, easy to administer, and has promise to widen the scope of populations with GI disorders for which clinicians can screen patients, diagnose disorders, and refine treatments objectively

Re-entrant Layer-by-Layer Etching of GaAs(001)

We report the first observation of re-entrant layer-by-layer etching based on {\it in situ\/} reflection high-energy electron-diffraction measurements. With AsBr$_3$ used to etch GaAs(001), sustained specular-beam intensity oscillations are seen at high substrate temperatures, a decaying intensity with no oscillations at intermediate temperatures, but oscillations reappearing at still lower temperatures. Simulations of an atomistic model for the etching kinetics reproduce the temperature ranges of these three regimes and support an interpretation of the origin of this phenomenon as the site-selectivity of the etching process combined with activation barriers to interlayer adatom migration.Comment: 11 pages, REVTeX 3.0. Physical Review Letters, in press

The Extended Shapes of Galactic Satellites

We are exploring the extended stellar distributions of Galactic satellite galaxies and globular clusters. For seven objects studied thus far, the observed profile departs from a King function at large r, revealing a ``break population'' of stars. In our sample, the relative density of the ``break'' correlates to the inferred M/L of these objects. We discuss opposing hypotheses for this trend: (1) Higher M/L objects harbor more extended dark matter halos that support secondary, bound, stellar ``halos''. (2) The extended populations around dwarf spheroidals (and some clusters) consist of unbound, extratidal debris from their parent objects, which are undergoing various degrees of tidal disruption. In this scenario, higher M/L ratios reflect higher degrees of virial non-equilibrium in the parent objects, thus invalidating a precept underlying the use of core radial velocities to obtain masses.Comment: 8 pages, including 2 figures Yale Cosmology Workshop: The Shapes of Galaxies and Their Halo

A Simplified Approach for Estimating Soil Carbon and Nitrogen Stocks in Semi-Arid Complex Terrain

We investigated soil carbon (C) and nitrogen (N) distribution and developed a model, using readily available geospatial data, to predict that distribution across a mountainous, semi-arid, watershed in southwestern Idaho (USA). Soil core samples were collected and analyzed from 133 locations at 6 depths (n=798), revealing that aspect dramatically influences the distribution of C and N, with north-facing slopes exhibiting up to 5 times more C and N than adjacent southfacing aspects. These differences are superimposed upon an elevation (precipitation) gradient, with soil C and N contents increasing by nearly a factor of 10 from the bottom (1100 m elevation) to the top (1900 m elevation) of the watershed. Among the variables evaluated, vegetation cover, as represented by a Normalized Difference Vegetation Index (NDVI), is the strongest, positively correlated, predictor of C; potential insolation (incoming solar radiation) is a strong, negatively correlated, secondary predictor. Approximately 62% (as R2) of the variance in the C data is explained using NDVI and potential insolation, compared with an R2 of 0.54 for a model using NDVI alone. Soil N is similarly correlated to NDVI and insolation. We hypothesize that the correlations between soil C and N and slope, aspect and elevation reflect, in part, the inhibiting influence of insolation on semi-arid ecosystem productivity via water limitation. Based on these identified relationships, two modeling techniques (multiple linear regression and cokriging) were applied to predict the spatial distribution of soil C and N across the watershed. Both methods produce similar distributions, successfully capturing observed trends with aspect and elevation. This easily applied approach may be applicable to other semi-arid systems at larger scales