TensorFlow on state-of-the-art HPC clusters: a machine learning use case

The recent rapid growth of the data-flow programming paradigm enabled the development of specific architectures, e.g., for machine learning. The most known example is the Tensor Processing Unit (TPU) by Google. Standard data-centers, however, still can not foresee large partitions dedicated to machine learning specific architectures. Within data-centers, the High-Performance Computing (HPC) clusters are highly parallel machines targeting a broad class of compute-intensive workflows, as such they can be used for tackling machine learning challenges. On top of this, HPC architectures are rapidly changing, including accelerators and instruction sets other than the classical x86 CPUs. In this blurry scenario, identifying which are the best hardware/software configurations to efficiently support machine learning workloads on HPC clusters is not trivial. In this paper, we considered the workflow of TensorFlow for image recognition. We highlight the strong dependency of the performance in the training phase on the availability of arithmetic libraries optimized for the underlying architecture. Following the example of Intel leveraging the MKL libraries for improving the TensorFlow performance, we plugged the Arm Performance Libraries into TensorFlow and tested on an HPC cluster based on Marvell ThunderX2 CPUs. Also, we performed a scalability study on three state-of-the-art HPC clusters based on different CPU architectures, x86 Intel Skylake, Arm-v8 Marvell ThunderX2, and PowerPC IBM Power9.Postprint (author's final draft

Computational Fluid and Particle Dynamics Simulations for Respiratory System: Runtime Optimization on an Arm Cluster

Computational fluid and particle dynamics simulations (CFPD) are of paramount importance for studying and improving drug effectiveness. Computational requirements of CFPD codes involves high-performance computing (HPC) resources. For these reasons we introduce and evaluate in this paper system software techniques for improving performance and tolerate load imbalance on a state-of-the-art production CFPD code. We demonstrate benefits of these techniques on both Intel- and Arm-based HPC clusters showing the importance of using mechanisms applied at runtime to improve the performance independently of the underlying architecture. We run a real CFPD simulation of particle tracking on the human respiratory system, showing performance improvements of up to 2X, keeping the computational resources constant.This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology project (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European Mont-Blanc projects (288777, 610402 and 671697).Peer ReviewedPostprint (author's final draft

Observações sobre a produção multipla de pions por hadrons da radiação cosmica

Orientador: Cesare Mansueto GiulioTese (doutorado) - Universidade Estadual de Campinas Instituto de Fisica Gleb WataghinResumo: Não informadoAbstract: Not informed.DoutoradoFísicaDoutor em Ciência

Runtime Mechanisms to Survive New HPC Architectures: A Use-Case in Human Respiratory Simulations

Computational Fluid and Particle Dynamics (CFPD) simulations are of paramount importance for studying and improving drug effectiveness. Computational requirements of CFPD codes demand high-performance computing (HPC) resources. For these reasons we introduce and evaluate in this paper system software techniques for improving performance and tolerate load imbalance on a state-of-the-art production CFPD code. We demonstrate benefits of these techniques on Intel-, IBM-, and Arm-based HPC technologies ranked in the Top500 supercomputers, showing the importance of using mechanisms applied at runtime to improve the performance independently of the underlying architecture. We run a real CFPD simulation of particle tracking on the human respiratory system, showing performance improvements of up to 2x, across different architectures, while applying runtime techniques and keeping constant the computational resources.This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology project (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European Mont-Blanc projects (288777, 610402 and 671697).Peer ReviewedPreprin

Management of the violent or agitated patient

OBJETIVO: Revisar as medidas preconizadas para o manejo de pacientes agitados ou agressivos. MÉTODO: Por meio de uma busca em bancos de dados (PubMed e Web of Science) foram identificados artigos empíricos e revisões sobre intervenções farmacológicas e não farmacológicas para o manejo de agitação e/ou violência. RESULTADOS: O manejo não farmacológico de agitação/agressão engloba a organização do espaço físico e a adequação de atitudes e comportamentos dos profissionais de saúde. O objetivo principal do manejo farmacológico é a tranquilização rápida, buscando a redução dos sintomas de agitação e agressividade, sem a indução de sedação profunda ou prolongada, mantendo-se o paciente tranquilo, mas completa ou parcialmente responsivo. A polifarmácia deve ser evitada e as doses das medicações devem ser o menor possível, ajustadas de acordo com a necessidade clínica. A administração intramuscular de medicação deve ser considerada como última alternativa e as opções de uso de antipsicóticos e benzodiazepínicos são descritas e comentadas. O manejo físico, por meio de contenção mecânica, pode ser necessário nas situações de violência em que exista risco para o paciente ou equipe, e deve obedecer a critérios rigorosos. CONCLUSÃO: Os procedimentos devem ser cuidadosamente executados, evitando complicações de ordem física e emocional para pacientes e equipe.OBJECTIVE: To review current data about the management of agitated or aggressive patients. METHOD: Through a search of databases (PubMed and Web of Science), empirical articles and reviews about pharmacological and non-pharmacological interventions for the management of agitation and /or violence were identified. RESULTS: The non-pharmacological management of agitation/aggression encompasses the organization of space and appropriateness of behavior and attitudes of health professionals. The main goal of pharmacological management is rapid tranquilization aimed at reducing symptoms of agitation and aggression, without the induction of deep or prolonged sedation, keeping the patient calm, but completely or partially responsive. Polypharmacy should be avoided, and doses of medications should be as small as possible, adjusted according to clinical need. Intramuscular administration of medication should be considered as a last resort and the options for the use of antipsychotics and benzodiazepines are described and commented. The physical management by means of mechanical restraint may be necessary in violent situations where there is risk to the patient or staff, and must meet strict criteria. CONCLUSION: Procedures must be carefully implemented to avoid physical and emotional complications for patients and staff

Tectonic insights of the southwest Amazon Craton from geophysical, geochemical and mineralogical data of Figueira Branca mafic-ultramafic suite, Brazil

This work was done with the support of the CNPq, National Council for Technological and Scientific Development – Brazil [grant numbers 443355/2014-2, 200473/2015-8, 141587/2013-0]; Peter A. Cawood acknowledges support from the Australian Research Council [grant number FL160100168].The Figueira Branca Suite is a layered mafic-ultramafic complex in the Jauru Terrane, southwest Amazon Craton. New lithological, geochemical, gamma-ray and potential field data, integrated with geological, isotope and paleomagnetic data are used to characterize this pulse of Mesoproterozoic extension-related magmatism. The Figueira Branca Suite formed through juvenile magma emplacement into the crust at 1425 Ma, coeval with the later stages of the Santa Helena Orogen. Gabbros and peridotite-gabbros display increasing enrichment of LREE, interpreted as evidence of progressive fractionation of the magma. Magnetic and gamma-ray data delimit the extent of magmatism within the suite to four bodies to the north of Indiavaí city. Modelling gravity and magnetic field data indicate that the anomalous sources are close to the surface or outcropping. These intrusions trend northwest over 8 km, with significant remanent magnetization that is consistent with published direction obtained through paleomagnetic data. The emplacement, mineralogy and geochemical signature point towards a back-arc extension tectonic framework in the later stages of the Santa Helena Orogen.PostprintPeer reviewe

O Parque CienTec–USP e o ano internacional do planeta Terra — AIPT

The ONU declaration in 2005 of the International Year of Planet Earth — IYPE allowed the CienTec Park to perform some activities in Brazil. The CienTec Park organized two types of activities: one for a specific public with previous knowledge of the subject and another for the public in general. The activities were of two kinds: one with scientific researchers and specialists debating questions about urban parks in 2006; the other was for the public in general with lectures about the geophysical phenomena and its relation to the human life, performed in 2007. Other activity was the organization of a digital data bank about the recent scientific production on geophysical phenomena, in phase of development. This article is about the public activities, either for researchers  and  specialists and for the public in general.A definição pela ONU em 2005 de um Ano Internacional do Planeta Terra — AIPT permitiu ao Parque CienTec–USP a inserção nas atividades desenvolvidas no país, que podem ser sintetizadas em alguns itens, que foram estruturados em dois conjuntos: um deles é o da externalização de questões científicas tanto para um público especializado, como o seminário discutindo as condi-ções de funcionamento dos Parques Urbanos em 2006, como ao grande público de estudantes e interessados, sob forma de palestras de divulgação científica sobre alguns fenômenos geofísicos e a sua relação com as condições de vida humana em 2007. O segundo conjunto, internalizado, foi o de organização de um banco de dados informatizado, sobre a produção científica dos assuntos referentes ao tema, estruturado, em fase de alimentação de dados. Este artigo relata as atividades destinadas ao público, quer o especializado, quer o grande públic

Special topics on magmatic petrology

The technological development of the last decades allowed great advances in analytical processes, both in variety and speed of results. Sophisticated instruments, highly-developed chemical processes and the use of computers have enabled quantizing elements and isotopes that are concentrated in minerals based on the magmatic processes involved. In 2010, the lead author of this text taught a course at the Geosciences Institute of the University of Sao Paulo on the most recent subjects in petrology, complemented with computer programs for specific applications. The success of that course suggested the need to collect his lecture notes in an organized format, so as to make them available to the scientific community. This text, organized in twenty separate topics, is designed to complement the basic knowledge in the area of petrology.O desenvolvimento tecnológico das últimas décadas permitiu um grande avanço dos processos analíticos, tanto quanto à variedade como à rapidez na obtenção dos resultados. Instrumentos sofisticados, processos químicos refinados e o uso de computadores possibilitaram quantizar elementos e isótopos concentrados nos minerais de acordo com os processos magmáticos envolvidos. Em 2010, o primeiro autor deste texto ministrou um curso no Instituto de Geociências da Universidade de São Paulo sobre os temas mais recentes de interesse petrológico, complementado por programas de cálculo de interesse específico. O sucesso do curso levou à ideia de reunir as anotações das aulas ministradas e elaboradas pelo autor para colocar tal conteúdo à disposição da comunidade científica. Em vinte tópicos, o texto visa apenas complementar os conhecimentos básicos já adquiridos

Contribuição geofísica ao estudo do Batólito Granítico Santa Helena, sudoeste do Cráton Amazônico

O Batólito Santa Helena é alvo de muitas divergências referentes à sua extensão geográfica, constituição litológica, caracterização geoquímica e ambiente geotectônico. Este trabalho visa, a partir da utilização de dados geofísicos (gamaespectrometria e aeromagnetometria), contribuir para um melhor entendimento dessa intrusão. Os dados aerogeofísicos utilizados foram obtidos através da Companhia de Pesquisa e Recursos Minerais, atual Serviço Geológico do Brasil (CPRM), que contratou os aerolevantamentos sobre a região estudada. Diante da variedade composicional das rochas que compõem o batólito, foram analisados o contraste de susceptibilidade (magnetometria) e a variação de distribuição dos radioelementos (K, Th e U, medidos por gamaespectrometria). A assinatura geofísica resultante apresenta diferenças entre a parte norte e sul do Batólito Santa Helena, sugerindo sua divisão em duas partes distintas. O limite entre essas duas suítes internas coincide com a localização de um sistema de lineamentos magnéticos que se estendem através do batólito com direção aproximadamente N75°W.The Santa Helena batholith is subject of many controversies concerning its geographical extension, lithological constitution, geochemical characterization and geotectonic setting. This paper aims to contribute for a better understanding of this intrusion using geophysical data (gammaspectrometric and aeromagnetic). These data were obtained through surveys contracted by the Geological Survey of Brazil (CPRM) flown over the study region. Given the compositional variety of the rocks, we analyzed the susceptibility contrast (magnetometry) and distribution of radioelements (K, Th and U, measured by gammaspectrometry) in the batholith. The resulting geophysical signature is different when comparing the northern and southern parts of the body, suggesting the presence of two distinct suites. The boundary between these two suites coincides with the location of an approximately N75°W oriented fault system that extends through the batholith