Tuning EASY-Backfilling Queues

International audienceEASY-Backfilling is a popular scheduling heuristic for allocating jobs in large scale High Performance Computing platforms. While its aggressive reservation mechanism is fast and prevents job starvation, it does not try to optimize any scheduling objective per se. We consider in this work the problem of tuning EASY using queue reordering policies. More precisely, we propose to tune the reordering using a simulation-based methodology. For a given system, we choose the policy in order to minimize the average waiting time. This methodology departs from the First-Come, First-Serve rule and introduces a risk on the maximum values of the waiting time, which we control using a queue thresholding mechanism. This new approach is evaluated through a comprehensive experimental campaign on five production logs. In particular, we show that the behavior of the systems under study is stable enough to learn a heuristic that generalizes in a train/test fashion. Indeed, the average waiting time can be reduced consistently (between 11% to 42% for the logs used) compared to EASY, with almost no increase in maximum waiting times. This work departs from previous learning-based approaches and shows that scheduling heuristics for HPC can be learned directly in a policy space

Improving Backfilling by using Machine Learning to predict Running Times

International audienceThe job management system is the HPC middleware responsible for distributing computing power to applications. While such systems generate an ever increasing amount of data, they are characterized by uncertainties on some parameters like the job running times. The question raised in this work is: To what extent is it possible/useful to take into account predictions on the job running times for improving the global scheduling? We present a comprehensive study for answering this question assuming the popular EASY backfilling policy. More precisely, we rely on some classical methods in machine learning and propose new cost functions well-adapted to the problem. Then, we assess our proposed solutions through intensive simulations using several production logs. Finally, we propose a new scheduling algorithm that outperforms the popular EASY backfilling algorithm by 28% considering the average bounded slowdown objective

A protocol for ultra-high field laminar fMRI in the human brain.

Ultra-high field (UHF) neuroimaging affords the sub-millimeter resolution that allows researchers to interrogate brain computations at a finer scale than that afforded by standard fMRI techniques. Here, we present a step-by-step protocol for using UHF imaging (Siemens Terra 7T scanner) to measure activity in the human brain. We outline how to preprocess the data using a pipeline that combines tools from SPM, FreeSurfer, ITK-SNAP, and BrainVoyager and correct for vasculature-related confounders to improve the spatial accuracy of the fMRI signal. For complete details on the use and execution of this protocol, please refer to Jia et al. (2020) and Zamboni et al. (2020).This work was supported by grants to Z.K. from the Biotechnology and Biological Sciences Research Council (H012508 and BB/P021255/1), the Wellcome Trust (205067/Z/16/Z) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 840271

A protocol for ultra-high field laminar fMRI in the human brain.

Ultra-high field (UHF) neuroimaging affords the sub-millimeter resolution that allows researchers to interrogate brain computations at a finer scale than that afforded by standard fMRI techniques. Here, we present a step-by-step protocol for using UHF imaging (Siemens Terra 7T scanner) to measure activity in the human brain. We outline how to preprocess the data using a pipeline that combines tools from SPM, FreeSurfer, ITK-SNAP, and BrainVoyager and correct for vasculature-related confounders to improve the spatial accuracy of the fMRI signal. For complete details on the use and execution of this protocol, please refer to Jia et al. (2020) and Zamboni et al. (2020).This work was supported by grants to Z.K. from the Biotechnology and Biological Sciences Research Council (H012508 and BB/P021255/1), the Wellcome Trust (205067/Z/16/Z) and European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska Curie grant agreement No 840271

Recurrent Processing Drives Perceptual Plasticity.

Learning and experience are critical for translating ambiguous sensory information from our environments to perceptual decisions. Yet evidence on how training molds the adult human brain remains controversial, as fMRI at standard resolution does not allow us to discern the finer scale mechanisms that underlie sensory plasticity. Here, we combine ultra-high-field (7T) functional imaging at sub-millimeter resolution with orientation discrimination training to interrogate experience-dependent plasticity across cortical depths that are known to support dissociable brain computations. We demonstrate that learning alters orientation-specific representations in superficial rather than middle or deeper V1 layers, consistent with recurrent plasticity mechanisms via horizontal connections. Further, learning increases feedforward rather than feedback layer-to-layer connectivity in occipito-parietal regions, suggesting that sensory plasticity gates perceptual decisions. Our findings reveal finer scale plasticity mechanisms that re-weight sensory signals to inform improved decisions, bridging the gap between micro- and macro-circuits of experience-dependent plasticity

"Knees" in lithium-ion battery aging trajectories

Lithium-ion batteries can last many years but sometimes exhibit rapid, nonlinear degradation that severely limits battery lifetime. In this work, we review prior work on "knees" in lithium-ion battery aging trajectories. We first review definitions for knees and three classes of "internal state trajectories" (termed snowball, hidden, and threshold trajectories) that can cause a knee. We then discuss six knee "pathways", including lithium plating, electrode saturation, resistance growth, electrolyte and additive depletion, percolation-limited connectivity, and mechanical deformation -- some of which have internal state trajectories with signals that are electrochemically undetectable. We also identify key design and usage sensitivities for knees. Finally, we discuss challenges and opportunities for knee modeling and prediction. Our findings illustrate the complexity and subtlety of lithium-ion battery degradation and can aid both academic and industrial efforts to improve battery lifetime.Comment: Submitted to the Journal of the Electrochemical Societ

Evaluation of MLH1 variants of unclear significance

Inactivating mutations in the MLH1 gene cause the cancer predisposition Lynch syndrome, but for small coding genetic variants it is mostly unclear if they are inactivating or not. Nine such MLH1 variants have been identified in South American colorectal cancer (CRC) patients (p.Tyr97Asp, p.His112Gln, p.Pro141Ala, p.Arg265Pro, p.Asn338Ser, p.Ile501del, p.Arg575Lys, p.Lys618del, p.Leu676Pro), and evidence of pathogenicity or neutrality was not available for the majority of these variants. We therefore performed biochemical laboratory testing of the variant proteins and compared the results to protein in silico predictions on structure and conservation. Additionally, we collected all available clinical information of the families to come to a conclusion concerning their pathogenic potential and facilitate clinical diagnosis in the affected families. We provide evidence that four of the alterations are causative for Lynch syndrome, four are likely neutral and one shows compromised activity which can currently not be classified with respect to its pathogenic potential. The work demonstrates that biochemical testing, corroborated by congruent evolutionary and structural information, can serve to reliably classify uncertain variants when other data are insufficient.Barretos Cancer Hospital was partially funded by FINEP‐CT‐INFRA, Grant Number: 02/2010, Radium Hospital Foundation (Oslo, Norway), Helse Sør‐Øst (Norway); Deutsche Forschungsgemeinschaft, Grant Number: PL688/2‐1info:eu-repo/semantics/publishedVersio

Eventos de Influência do Buraco de Ozônio Antártico Ocorridos em 2016 Sobre o Sul do Brasil

O presente trabalho objetivou identificar e analisar a dinâmica estratosférica dos eventos de influência do Buraco de Ozônio Antártico (BOA) ocorridos sobre o Sul do Brasil no ano de 2016. Para atingir esse objetivo, buscou-se dias de redução no conteúdo de ozônio estratosférico com base em dados médios diários da Coluna Total de Ozônio (CTO) obtidos pelo espectrofotômetro Brewer instalado no Observatório Espacial do Sul (OES/INPE) (29.443752 ºS, 53.823084 ºO; 488,7 metros) e pelo instrumento de medição de Ozônio (Ozone Monitoring Instrument - OMI) a bordo do satélite Aura da NASA.  Para esses dias foram realizadas análises da dinâmica da estratosfera através de campos isentrópicos de Vorticidade Potencial (PV) nos níveis de 600 e 700 K de temperatura potencial, utilizando as médias diárias de PV obtidas a partir das reanálises ERA-Interim do ECMWF (European Centre for Medium-range Weather Forecast) a fim de verificar a origem das massas de ar pobres em ozônio, e desta forma, a confirmação da origem dessas massas através das trajetórias retroativas obtidas com uso do modelo HYSPLIT (HYbrid Single-Particle Lagrangian Integrated Trajectory) da NOAA (National Oceanic and Atmospheric Administration). Além disso, imagens do conteúdo de ozônio do satélite OMI foram utilizadas como técnica complementar para verificar a atuação do BOA sobre o Sul do Brasil. Usando a metodologia apresentada identificou-se 6 eventos de influência do Buraco de Ozônio Antártico sobre o Sul do Brasil no ano de 2016 com percentagem de redução média de 11%  da CTO em relação as climatologias mensais, confirmados pela passagem de filamentos polares estratosféricos sobre a região do OES, observados nos campos isentrópicos de VP nos níveis de 600 e 700 K de temperatura potencial assim como pelas trajetórias retroativas de origem polar obtidas no modelo HYSPLIT

Ação do PIBID Biologia na Educação Básica através da abordagem temática Feireana: ações formativas na educação ambiental

This paper shares the experience of reflective thinking about a training process for teachers and students that was made viable by a program of the Brazilian federal government, the Institutional Program for Scholarships for Initiation in Teaching (pibid, for its initials in Portuguese) through a partnership between universities and basic education schools. In this case, the pibid team diagnosed the need to know the reality of students of the Profesor Benedicto Leme Vieira Neto State School (Salto de Pirapora, São Paulo, Brazil) and their views about their surroundings. The purpose of this study is to describe and analyze, from a critical standpoint, the education process that took place between 2014 and 2015 through the action-research approach known as Freire’s thematic approach and a qualitative questionnaire answered by two students from each classroom, for a total of 33 answered questionnaires. Each response was evaluated, and the following situations that limit better living conditions were obtained: environmental problems, consequent risks to the health of the community, dissatisfaction with the environments intended for leisure, lack of identification with the school environment and its surroundings. By identifying these situations, we were able to plan and develop training activities at school, with the aim of articulating teachers in higher education, basic education and initial training. We problematized the notion that the problems observed are not individual and that they affect everyone. As a result, we observed the positive impact of the training activities promoted by the pibid team and the school community, and on the development of pedagogical workshops to continue the work.El presente artículo consiste en un relato de experiencia de cuño reflexivo en tornoa un proceso de formación de profesores y alumnos viabilizado por un programa delgobierno federal brasileño - PIBID (Programa Institucional de Beca de Iniciación a laDocencia) - a través del establecimiento de la asociación entre universidades y escuelasde educación básica. En este caso, el equipo del PIBID diagnosticó la necesidad deconocer la realidad vivida por los alumnos de la Escuela Estadual Profesor BenedictoLeme Vieira Neto (Salto de Pirapora – São Paulo – Brasil) y sus concepciones sobre el ambiente que les rodea. Este estudio tiene como objetivo describir y analizar críticamente el proceso de formación que se desarrolló entre 2014 y 2015 a través de la metodología de investigación-acción denominada abordaje temático Freireano y de un cuestionario cualitativo aplicado a dos alumnos de cada aula, en un total de 33 cuestionarios respondidos. Se evaluó cada respuesta y se obtuvieram las siguientes situaciones limitantes de mejores condiciones de vida: problemas ambientales, consecuentes riesgos a la salud de la comunidad, descontento con los ambientes destinados al ocio, falta de identificación con el medio ambiente escolar y sus alrededores. La identificación de estas situaciones permitió la planificación y desarrollo de actividades de formación en la escuela, con el fin de articular los profesores en la educación superior, la educación básica y la formación inicial. Se problematizó la noción de que los problemas observados no son individuales, y afecta a todos. Como resultado fue observado el impacto positivo de las actividades formativas propiciadas por el equipo PIBID, junto a comunidad de la escuela, y en el desarrollo de talleres pedagógicos para la continuidad del trabajo.O presente artigo consiste em um relato de experiência de cunho reflexivo sobre o processo de formação de professores e alunos viabilizado por um programa do governo federal brasileiro — pibid (programa institucional de bolsa de iniciação à docência)- Através do estabelecimento da associação entre universidades e escolas de Educação Básica. Neste caso, a equipe do pibid diagnosticou a necessidade de conhecer a realidade vivenciada pelos alunos da Escola Estadual Professor Benedicto Leme Vieira Neto (Salto de Pirapora, São Paulo, Brasil) e suas concepções sobre o ambiente que os rodeia. Este estudo tem como objetivo descrever e analisar criticamente o processo de formação desenvolvido entre 2014 e 2015, através da metodologia de pesquisa-ação denominada abordagem temática Feireana e um questionário qualitativo aplicado a dois alunos de cada sala de aula, em total 33 questionários respondidos. Avaliou-se cada resposta e obtiveram-se as seguintes situações limitantes de melhores condições de vida: problemas ambientais, consequentes riscos à saúde da comunidade, desconformidade com os ambientes destinados ao lazer, falta de identificação como o ambiente escolar e suas proximidades. A identificação dessas situações possibilitou a planificação e o desenvolvimento de atividades de formação na escola, visando articular os professores na educação superior, o ensino básico e a formação inicial. Problematizou-se a noção de que os problemas observados não são individuais e a afetam à comunidade. Como resultado, evidenciou-se o impacto positivo das atividades formativas propiciadas pela equipe pibid, em parceria com a comunidade da escola, no desenvolvimento de oficinas pedagógicas para a continuidade do trabalho

Estudo de tendência do consumo de psicofármacos em município de Minas Gerais sob risco geológico

O objetivo deste trabalho foi analisar a tendência do consumo de psicofármacos por usuários do Sistema Único de Saúde em município sob risco geológico (Congonhas, Minas Gerais). Trata-se de um estudo farmacoepidemiológico descritivo, do tipo estudo quantitativo de consumo, referente à utilização de psicofármacos. Uma análise descritiva completa dos psicofármacos dispensados foi realizada para os períodos globais antes (2018) e após (2019) o rompimento da barragem de Brumadinho, de acordo com os princípios ativos e grandes classes terapêuticas (antidepressivos e benzodiazepínicos). As quantidades dispensadas nos dois períodos propostos foram ainda descritas de acordo com o sexo do paciente e com o risco de inundação da região da unidade de atenção primária à saúde do participante em caso de rompimento de barragem. Os resultados mostraram um aumento no total e na média de unidades dispensadas por dia útil com estoque disponível de antidepressivos (aumento de 0,6% e 5,2%, respectivamente). Por outro lado, no que se refere aos benzodiazepínicos, identificou-se redução no total e na média de unidades dispensadas por dia útil com estoque disponível (redução de 7,2% e 3,3%, respectivamente). O estudo possibilitou conhecer a tendência de consumo desses medicamentos visando a uma melhor reorganização da assistência farmacêutica do município de Congonhas ante os novos desafios impostos pela realidade geológica