PMCTrack: Delivering performance monitoring counter support to the OS scheduler

Hardware performance monitoring counters (PMCs) have proven effective in characterizing application performance. Because PMCs can only be accessed directly at the OS privilege level, kernellevel tools must be developed to enable the end-user and userspace programs to access PMCs. A large body of work has demonstrated that the OS can perform effective runtime optimizations in multicore systems by leveraging performance-counter data. Special attention has been paid to optimizations in the OS scheduler. While existing performance monitoring tools greatly simplify the collection of PMC application data from userspace, they do not provide an architecture-agnostic kernel-level mechanism that is capable of exposing high-level PMC metrics to OS components, such as the scheduler. As a result, the implementation of PMC-based OS scheduling schemes is typically tied to specific processor models. To address this shortcoming we present PMCTrack, a novel tool for the Linux kernel that provides a simple architecture-independent mechanism that makes it possible for the OS scheduler to access per-thread PMC data. Despite being an OSoriented tool, PMCTrack still allows the gathering of monitoring data from userspace, enabling kernel developers to carry out the necessary offline analysis and debugging to assist them during the scheduler design process. In addition, the tool provides both the OS and the user-space PMCTrack components with other insightful metrics available in modern processors and which are not directly exposed as PMCs, such as cache occupancy or energy consumption. This information is also of great value when it comes to analyzing the potential benefits of novel scheduling policies on real systems. In this paper, we analyze different case studies that demonstrate the flexibility, simplicity and powerful features of PMCTrack.Facultad de InformáticaInstituto de Investigación en Informátic

PMCTrack: Delivering performance monitoring counter support to the OS scheduler

Hardware performance monitoring counters (PMCs) have proven effective in characterizing application performance. Because PMCs can only be accessed directly at the OS privilege level, kernellevel tools must be developed to enable the end-user and userspace programs to access PMCs. A large body of work has demonstrated that the OS can perform effective runtime optimizations in multicore systems by leveraging performance-counter data. Special attention has been paid to optimizations in the OS scheduler. While existing performance monitoring tools greatly simplify the collection of PMC application data from userspace, they do not provide an architecture-agnostic kernel-level mechanism that is capable of exposing high-level PMC metrics to OS components, such as the scheduler. As a result, the implementation of PMC-based OS scheduling schemes is typically tied to specific processor models. To address this shortcoming we present PMCTrack, a novel tool for the Linux kernel that provides a simple architecture-independent mechanism that makes it possible for the OS scheduler to access per-thread PMC data. Despite being an OSoriented tool, PMCTrack still allows the gathering of monitoring data from userspace, enabling kernel developers to carry out the necessary offline analysis and debugging to assist them during the scheduler design process. In addition, the tool provides both the OS and the user-space PMCTrack components with other insightful metrics available in modern processors and which are not directly exposed as PMCs, such as cache occupancy or energy consumption. This information is also of great value when it comes to analyzing the potential benefits of novel scheduling policies on real systems. In this paper, we analyze different case studies that demonstrate the flexibility, simplicity and powerful features of PMCTrack.Facultad de InformáticaInstituto de Investigación en Informátic

The Influence Of An External Dc Substrate Bias On The Density Of States In Hydrogenated Amorphous Silicon

We report a study of the dependence of the density of states in hydrogenated amorphous silicon produced under different dc substrate biases. A dependence of the density of states in materials deposited simultaneously onto indium-tin-oxide-coated glass and stainless steel has been found. The same is attributed to sheath plasma differences at the top surface of the growing film. The density of states was determined by the space-charge-limited current method. The universal scaling law is tested for samples having a similar density of states. Attempts were made to correlate the product of the hole mobility and the recombination time for samples deposited in conditions similar to those used in the space-charge-limited current experiments.65124869487

Evaluation of liquid biphasic Granada medium and instant liquid biphasic Granada medium for group B streptococcus detection.

INTRODUCTION: Group B streptococci (GBS) are transmitted from the mother to the newborn. Prevention of neonatal infection is achieved by intrapartum prophylaxis given to mothers colonized with GBS at 35 to 37 weeks of pregnancy. MATERIALS AND METHODS: Liquid biphasic Granada medium (LB) and instant liquid biphasic Granada medium (ILB) were evaluated for GBS detection. Vaginal swabs obtained from 300 women were inoculated onto LB or ILB, or onto Todd-Hewitt broth and analyzed with the ATB system (comparison method). RESULTS: Prevalence of GBS was 20% (61/300). LB and Todd-Hewitt with ATB detected GBS in 20% of women, and ILB in 19% of women. No growth was observed at four hours in any of the media studied. At 10 h and 14 h, identification of GBS was possible in 43/300 (14%) and 53/300 (18%) of ILB cultures, respectively, and in 32/300 (11%) and 46/300 (15%) of LB cultures. CONCLUSION: All the media used are suitable for GBS detection. The majority of GBS were identified in ILB and LB cultures at 10 h and 14 h

PMCTrack: Delivering performance monitoring counter support to the OS scheduler

Hardware performance monitoring counters (PMCs) have proven effective in characterizing application performance. Because PMCs can only be accessed directly at the OS privilege level, kernellevel tools must be developed to enable the end-user and userspace programs to access PMCs. A large body of work has demonstrated that the OS can perform effective runtime optimizations in multicore systems by leveraging performance-counter data. Special attention has been paid to optimizations in the OS scheduler. While existing performance monitoring tools greatly simplify the collection of PMC application data from userspace, they do not provide an architecture-agnostic kernel-level mechanism that is capable of exposing high-level PMC metrics to OS components, such as the scheduler. As a result, the implementation of PMC-based OS scheduling schemes is typically tied to specific processor models. To address this shortcoming we present PMCTrack, a novel tool for the Linux kernel that provides a simple architecture-independent mechanism that makes it possible for the OS scheduler to access per-thread PMC data. Despite being an OSoriented tool, PMCTrack still allows the gathering of monitoring data from userspace, enabling kernel developers to carry out the necessary offline analysis and debugging to assist them during the scheduler design process. In addition, the tool provides both the OS and the user-space PMCTrack components with other insightful metrics available in modern processors and which are not directly exposed as PMCs, such as cache occupancy or energy consumption. This information is also of great value when it comes to analyzing the potential benefits of novel scheduling policies on real systems. In this paper, we analyze different case studies that demonstrate the flexibility, simplicity and powerful features of PMCTrack.Facultad de InformáticaInstituto de Investigación en Informátic

The metabolic response of P. putida KT2442 producing high levels of polyhydroxyalkanoate under single- and multiple-nutrient-limited growth: Highlights from a multi-level omics approach

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas putida </it>KT2442 is a natural producer of polyhydroxyalkanoates (PHAs), which can substitute petroleum-based non-renewable plastics and form the basis for the production of tailor-made biopolymers. However, despite the substantial body of work on PHA production by <it>P. putida </it>strains, it is not yet clear how the bacterium re-arranges its whole metabolism when it senses the limitation of nitrogen and the excess of fatty acids as carbon source, to result in a large accumulation of PHAs within the cell. In the present study we investigated the metabolic response of KT2442 using a systems biology approach to highlight the differences between single- and multiple-nutrient-limited growth in chemostat cultures.</p> <p>Results</p> <p>We found that 26, 62, and 81% of the cell dry weight consist of PHA under conditions of carbon, dual, and nitrogen limitation, respectively. Under nitrogen limitation a specific PHA production rate of 0.43 (g·(g·h)^-1) was obtained. The residual biomass was not constant for dual- and strict nitrogen-limiting growth, showing a different feature in comparison to other <it>P. putida </it>strains. Dual limitation resulted in patterns of gene expression, protein level, and metabolite concentrations that substantially differ from those observed under exclusive carbon or nitrogen limitation. The most pronounced differences were found in the energy metabolism, fatty acid metabolism, as well as stress proteins and enzymes belonging to the transport system.</p> <p>Conclusion</p> <p>This is the first study where the interrelationship between nutrient limitations and PHA synthesis has been investigated under well-controlled conditions using a system level approach. The knowledge generated will be of great assistance for the development of bioprocesses and further metabolic engineering work in this versatile organism to both enhance and diversify the industrial production of PHAs.</p

NIR surface photometry of a sample of nearby spiral galaxies

The first results of an observational programme aimed at mapping a sample of face--on spiral galaxies in the NIR are presented. This paper shows the surface photometry of the first ten galaxies in the sample. The data were taken in the broad band $J$ (1.2 $\mu$m) and $K_{s}$ (2.2 $\mu$m) filters. The sources were selected mainly according to their size and brightness in order to suit the characteristics of the CAIN 2D NIR camera on the 1.5 m Carlos S\'anchez Telescope (Tenerife, Spain). The primary scientific goal is to provide a comprehensive and uniform database of the main structural and photometric parameters of the sample members from NIR surface photometry. To this end, elliptical isophotal fitting was performed on each galaxy image to extract information about the size and location of its morphological components and provide the azimuthally averaged radial brightness profile. Analytical functions for each component's brightness distribution were then used to match that profile, and their functional parameters obtained from the global fitting. This first report includes data for NGC 3344, NGC 3686, NGC 3938, NGC 3953, NGC 4254, NGC 4303, NGC 4314, NGC 5248, NGC 6384 and NGC 7479.Comment: 9 pages and 6 figures. Accepted for publication in A&

Evaluation of the PaO2/FiO2 ratio after cardiac surgery as a predictor of outcome during hospital stay

Background: the arterial partial pressure of O2 and the fraction of inspired oxygen (PaO2/FiO2) ratio is widely used in ICUs as an indicator of oxygenation status. Although cardiac surgery and ICU scores can predict mortality, during the first hours after cardiac surgery few instruments are available to assess outcome. The aim of this study was to evaluate the usefulness of PaO2/FIO2 ratio to predict mortality in patients immediately after cardiac surgery. Methods: we prospectively studied 2725 consecutive cardiac surgery patients between 2004 and 2009. PaO2/FiO2 ratio was measured on admission and at 3 h, 6 h, 12 h and 24 h after ICU admission, together with clinical data and outcomes. Results: all PaO2/FIO2 ratio measurements differed between survivors and non-survivors (p  242; Group 2, with PaO2/FIO2 from 202 to 242; and Group 3, with PaO2/FIO2 < 202. Group 3 showed higher in-ICU mortality and ICU length of stay and Groups 2 and 3 also showed higher respiratory complication rates. The presence of a PaO2/FIO2 ratio < 202 at 3 h after admission was shown to be a predictor of in-ICU mortality (OR:1.364; 95% CI:1.212-1.625, p < 0.001) and of worse long-term survival (88.8% vs. 95.8%; Log rank p = 0.002. Adjusted Hazard ratio: 1.48; 95% CI:1.293-1.786; p = 0.004). Conclusions: a simple determination of PaO2/FIO2 at 3 h after ICU admission may be useful to identify patients at risk immediately after cardiac surgery

Helminths of small rodents (Heteromyidae and Cricetidae) in the Yucatan Peninsula, Mexico: an integrative taxonomic approach to their inventory

In this survey, we inventoried the helminths of heteromyid and cricetid rodents captured in the Yucatan Peninsula from 2017 to 2019. Helminths were identified using morphological techniques (clearing, staining, and scanning electron microscopy). Also, the 28S rRNA gene of individuals from several helminth taxa was successfully amplified and sequenced. To confirm the identification at the generic level, and in some cases at the specific level, and the genealogical relationships of the parasites, phylogenetic analyses were performed with the new 28S sequences. We identified 22 species of helminths including three trematodes (Brachylaimidae, Dicrocoeliidae, and Microphallidae), five cestodes (Davaineidae, Hymenolepididae, and Taeniidae), and 14 nematodes (Trichuridae, Ancylostomatidae, Ornithostrongylidae, Heligmonellidae, and Oxyuridae) from Heteromys gaumeri (Heteromyidae), Ototylomys phyllotis, Oligoryzomys fulvescens, Peromyscus yucatanicus, Sigmodon toltecus, and Reithrodontomys gracilis (Cricetidae). The overall frequency of infection in small rodents was 84.1% (143/170); all specimens of H. gaumeri, S. toltecus and Ol. fulvescens were infected with helminths. In total, we provided 46 new sequences of the 28S gene from 17 species of helminths. Seven species are likely undescribed species, six are reported for the first time in rodents from Mexico, and 12 are new host records in the Americas. Before this study, 87 taxa of helminths had been reported from 35 cricetid and 12 heteromyid species in 21 Mexican states. Our findings increase to 93 the helminth taxa in these rodents, and to 36 the cricetid species parasitized by helminths. This large scale-survey is the first to use an integrative approach to inventory the helminths of wild small rodents in Mexico.Fil: Panti May, Jesús Alonso. Universidad Autónoma de Yucatán;Fil: Moguel Chin, Wilson Isaias. Universidad Autónoma de Yucatán;Fil: Hernández Mena, David Iván. Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional; MéxicoFil: Cárdenas-Vargas, Miguel Humberto. Universidad Autónoma de Yucatán; MéxicoFil: Torres Castro, Marco. Universidad Autónoma de Yucatán;Fil: García Prieto, Luis. Universidad Nacional Autónoma de México; MéxicoFil: Digiani, Maria Celina. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Zoología Invertebrados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Hernández Betancourt, Silvia F.. Universidad Autónoma de Yucatán;Fil: Vidal Martínez, Víctor Manuel. Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional; Méxic

New Results on Standard Solar Models

We describe the current status of solar modelling and focus on the problems originated with the introduction of solar abundance determinations with low CNO abundance values. We use models computed with solar abundance compilations obtained during the last decade, including the newest published abundances by Asplund and collaborators. Results presented here make focus both on helioseismic properties and the models as well as in the neutrino fluxes predictions. We also discuss changes in radiative opacities to restore agreement between helioseismology, solar models, and solar abundances and show the effect of such modifications on solar neutrino fluxes.Comment: 9 pages. Review talk presented at "Synergies between solar and stellar modelling", Rome, June 2009. To be published by Astrophysics and Space Scienc