Toward understanding I/O behavior in HPC workflows

Scientific discovery increasingly depends on complex workflows consisting of multiple phases and sometimes millions of parallelizable tasks or pipelines. These workflows access storage resources for a variety of purposes, including preprocessing, simulation output, and postprocessing steps. Unfortunately, most workflow models focus on the scheduling and allocation of com- putational resources for tasks while the impact on storage systems remains a secondary objective and an open research question. I/O performance is not usually accounted for in workflow telemetry reported to users. In this paper, we present an approach to augment the I/O efficiency of the individual tasks of workflows by combining workflow description frameworks with system I/O telemetry data. A conceptual architecture and a prototype implementation for HPC data center deployments are introduced. We also identify and discuss challenges that will need to be addressed by workflow management and monitoring systems for HPC in the future. We demonstrate how real-world applications and workflows could benefit from the approach, and we show how the approach helps communicate performance-tuning guidance to users

Metal-insulator transition from combined disorder and interaction effects in Hubbard-like electronic lattice models with random hopping

We uncover a disorder-driven instability in the diffusive Fermi liquid phase of a class of many-fermion systems, indicative of a metal-insulator transition of first order type, which arises solely from the competition between quenched disorder and interparticle interactions. Our result is expected to be relevant for sufficiently strong disorder in d = 3 spatial dimensions. Specifically, we study a class of half-filled, Hubbard-like models for spinless fermions with (complex) random hopping and short-ranged interactions on bipartite lattices, in d > 1. In a given realization, the hopping disorder breaks time reversal invariance, but preserves the special ``nesting'' symmetry responsible for the charge density wave instability of the ballistic Fermi liquid. This disorder may arise, e.g., from the application of a random magnetic field to the otherwise clean model. We derive a low energy effective field theory description for this class of disordered, interacting fermion systems, which takes the form of a Finkel'stein non-linear sigma model [A. M. Finkel'stein, Zh. Eksp. Teor. Fiz. 84, 168 (1983), Sov. Phys. JETP 57, 97 (1983)]. We analyze the Finkel'stein sigma model using a perturbative, one-loop renormalization group analysis controlled via an epsilon-expansion in d = 2 + epsilon dimensions. We find that, in d = 2 dimensions, the interactions destabilize the conducting phase known to exist in the disordered, non-interacting system. The metal-insulator transition that we identify in d > 2 dimensions occurs for disorder strengths of order epsilon, and is therefore perturbatively accessible for epsilon << 1. We emphasize that the disordered system has no localized phase in the absence of interactions, so that a localized phase, and the transition into it, can only appear due to the presence of the interactions.Comment: 47 pages, 25 figures; submitted to Phys. Rev. B. Long version of arXiv:cond-mat/060757

Comparison of the Value of Nursing Work Environments in Hospitals Across Different Levels of Patient Risk

Importance The literature suggests that hospitals with better nursing work environments provide better quality of care. Less is known about value (cost vs quality). Objectives To test whether hospitals with better nursing work environments displayed better value than those with worse nursing environments and to determine patient risk groups associated with the greatest value. Design, Setting, and Participants A retrospective matched-cohort design, comparing the outcomes and cost of patients at focal hospitals recognized nationally as having good nurse working environments and nurse-to-bed ratios of 1 or greater with patients at control group hospitals without such recognition and with nurse-to-bed ratios less than 1. This study included 25 752 elderly Medicare general surgery patients treated at focal hospitals and 62 882 patients treated at control hospitals during 2004-2006 in Illinois, New York, and Texas. The study was conducted between January 1, 2004, and November 30, 2006; this analysis was conducted from April to August 2015. Exposures Focal vs control hospitals (better vs worse nursing environment). Main Outcomes and Measures Thirty-day mortality and costs reflecting resource utilization. Results This study was conducted at 35 focal hospitals (mean nurse-to-bed ratio, 1.51) and 293 control hospitals (mean nurse-to-bed ratio, 0.69). Focal hospitals were larger and more teaching and technology intensive than control hospitals. Thirty-day mortality in focal hospitals was 4.8% vs 5.8% in control hospitals (P \u3c .001), while the cost per patient was similar: the focal-control was −$163 (95$542 to $215; P = .40), suggesting better value in the focal group. For the focal vs control hospitals, the greatest mortality benefit (17.3$941 per patient ($53 701 vs$52 760; P = .25). The greatest difference in value between focal and control hospitals appeared in patients in the second-highest risk quintile, with mortality of 4.2% vs 5.8% (P \u3c .001), with a nonsignificant cost difference of −$862 ($33 513 vs $34 375; P = .12). Conclusions and Relevance Hospitals with better nursing environments and above-average staffing levels were associated with better value (lower mortality with similar costs) compared with hospitals without nursing environment recognition and with below-average staffing, especially for higher-risk patients. These results do not suggest that improving any specific hospital’s nursing environment will necessarily improve its value, but they do show that patients undergoing general surgery at hospitals with better nursing environments generally receive care of higher value

Quasiparticle localization in superconductors with spin-orbit scattering

We develop a theory of quasiparticle localization in superconductors in situations without spin rotation invariance. We discuss the existence, and properties of superconducting phases with localized/delocalized quasiparticle excitations in such systems in various dimensionalities. Implications for a variety of experimental systems, and to the properties of random Ising models in two dimensions, are briefly discussed.Comment: 10 page

Examining Causes of Racial Disparities in General Surgical Mortality: Hospital Quality Versus Patient Risk

BACKGROUND: Racial disparities in general surgical outcomes are known to exist but not well understood. OBJECTIVES: To determine if black-white disparities in general surgery mortality for Medicare patients are attributable to poorer health status among blacks on admission or differences in the quality of care provided by the admitting hospitals. RESEARCH DESIGN: Matched cohort study using Tapered Multivariate Matching. SUBJECTS: All black elderly Medicare general surgical patients (N=18,861) and white-matched controls within the same 6 states or within the same 838 hospitals. MEASURES: Thirty-day mortality (primary); others include in-hospital mortality, failure-to-rescue, complications, length of stay, and readmissions. RESULTS: Matching on age, sex, year, state, and the exact same procedure, blacks had higher 30-day mortality (4.0% vs. 3.5%, P\u3c0.01), in-hospital mortality (3.9% vs. 2.9%, P\u3c0.0001), in-hospital complications (64.3% vs. 56.8% P\u3c0.0001), and failure-to-rescue rates (6.1% vs. 5.1% P\u3c0.001), longer length of stay (7.2 vs. 5.8 d, P\u3c0.0001), and more 30-day readmissions (15.0% vs. 12.5%, P\u3c0.0001). Adding preoperative risk factors to the above match, there was no significant difference in mortality or failure-to-rescue, and all other outcome differences were small. Blacks matched to whites in the same hospital displayed no significant differences in mortality, failure-to-rescue, or readmissions. CONCLUSIONS: Black and white Medicare patients undergoing the same procedures with closely matched risk factors displayed similar mortality, suggesting that racial disparities in general surgical mortality are not because of differences in hospital quality. To reduce the observed disparities in surgical outcomes, the poorer health of blacks on presentation for surgery must be addressed

Characteristics Associated With Differences in Survival Among Black and White Women With Breast Cancer

Importance Difference in breast cancer survival by race is a recognized problem among Medicare beneficiaries. Objective To determine if racial disparity in breast cancer survival is primarily attributable to differences in presentation characteristics at diagnosis or subsequent treatment. Design, Setting, and Patients Comparison of 7375 black women 65 years and older diagnosed between 1991 to 2005 and 3 sets of 7375 matched white control patients selected from 99 898 white potential controls, using data for 16 US Surveillance, Epidemiology and End Results (SEER) sites in the SEER-Medicare database. All patients received follow-up through December 31, 2009, and the black case patients were matched to 3 white control populations on demographics (age, year of diagnosis, and SEER site), presentation (demographics variables plus patient comorbid conditions and tumor characteristics such as stage, size, grade, and estrogen receptor status), and treatment (presentation variables plus details of surgery, radiation therapy, and chemotherapy). Main Outcomes and Measures 5-Year survival. Results The absolute difference in 5-year survival (blacks, 55.9%; whites, 68.8%) was 12.9% (95% CI, 11.5%-14.5%; P \u3c .001) in the demographics match. This difference remained unchanged between 1991 and 2005. After matching on presentation characteristics, the absolute difference in 5-year survival was 4.4% (95% CI, 2.8%-5.8%; P \u3c .001) and was 3.6% (95% CI, 2.3%-4.9%; P \u3c .001) lower for blacks than for whites matched also on treatment. In the presentation match, fewer blacks received treatment (87.4% vs 91.8%; P \u3c .001), time from diagnosis to treatment was longer (29.2 vs 22.8 days; P \u3c .001), use of anthracyclines and taxols was lower (3.7% vs 5.0%; P \u3c .001), and breast-conserving surgery without other treatment was more frequent (8.2% vs 7.3%; P = .04). Nevertheless, differences in survival associated with treatment differences accounted for only 0.81% of the 12.9% survival difference. Conclusions and Relevance In the SEER-Medicare database, differences in breast cancer survival between black and white women did not substantially change among women diagnosed between 1991 and 2005. These differences in survival appear primarily related to presentation characteristics at diagnosis rather than treatment differences

Noisy random resistor networks: renormalized field theory for the multifractal moments of the current distribution

We study the multifractal moments of the current distribution in randomly diluted resistor networks near the percolation treshold. When an external current is applied between to terminals $x$ and $x^\prime$ of the network, the $l$th multifractal moment scales as $M_I^{(l)} (x, x^\prime) \sim | x - x^\prime |^{\psi_l /\nu}$, where $\nu$ is the correlation length exponent of the isotropic percolation universality class. By applying our concept of master operators [Europhys. Lett. {\bf 51}, 539 (2000)] we calculate the family of multifractal exponents $\{\psi_l \}$ for $l \geq 0$ to two-loop order. We find that our result is in good agreement with numerical data for three dimensions.Comment: 30 pages, 6 figure

MicroRNA-regulated pathways of flow-stimulated angiogenesis and vascular remodeling in vivo

Background: Vascular shear stress promotes endothelial cell sprouting in vitro. The impact of hemodynamic forces on microRNA (miRNA) and gene expression within growing vascular networks in vivo, however, remain poorly investi‑ gated. Arteriovenous (AV) shunts are an established model for induction of neoangiogenesis in vivo and can serve as a tool for analysis of hemodynamic efects on miRNA and gene expression profles over time. Methods: AV shunts were microsurgically created in rats and explanted on postoperative days 5, 10 and 15. Neoan‑ giogenesis was confrmed by histologic analysis and micro-computed tomography. MiRNA and gene expression pro‑ fles were determined in tissue specimens from AV shunts by microarray analysis and quantitative real-time polymer‑ ase chain reaction and compared with sham-operated veins by bioinformatics analysis. Changes in protein expression within AV shunt endothelial cells were determined by immunohistochemistry. Results: Samples from AV shunts exhibited a strong overexpression of proangiogenic cytokines, oxygenationassociated genes (HIF1A, HMOX1), and angiopoetic growth factors. Signifcant inverse correlations of the expressions of miR-223-3p, miR-130b-3p, miR-19b-3p, miR-449a-5p, and miR-511-3p which were up-regulated in AV shunts, and miR-27b-3p, miR-10b-5p, let-7b-5p, and let-7c-5p, which were down-regulated in AV shunts, with their predicted interacting targets C–X–C chemokine receptor 2 (CXCR2), interleukin-1 alpha (IL1A), ephrin receptor kinase 2 (EPHA2), synaptojanin-2 binding protein (SYNJ2BP), forkhead box C1 (FOXC1) were present. CXCL2 and IL1A overexpression in AV shunt endothelium was confrmed at the protein level by immunohistochemistry. Conclusions: Our data indicate that fow-stimulated angiogenesis is determined by an upregulation of cytokines, oxygenation associated genes and miRNA-dependent regulation of FOXC1, EPHA2 and SYNJ2BP