Performance and Energy Trade-Offs for Parallel Applications on Heterogeneous Multi-Processing Systems

This work proposes a methodology to find performance and energy trade-offs for parallel applications running on Heterogeneous Multi-Processing systems with a single instruction-set architecture. These offer flexibility in the form of different core types and voltage and frequency pairings, defining a vast design space to explore. Therefore, for a given application, choosing a configuration that optimizes the performance and energy consumption is not straightforward. Our method proposes novel analytical models for performance and power consumption whose parameters can be fitted using only a few strategically sampled offline measurements. These models are then used to estimate an application’s performance and energy consumption for the whole configuration space. In turn, these offline predictions define the choice of estimated Pareto-optimal configurations of the model, which are used to inform the selection of the configuration that the application should be executed on. The methodology was validated on an ODROID-XU3 board for eight programs from the PARSEC Benchmark, Phoronix Test Suite and Rodinia applications. The generated Pareto-optimal configuration space represented a 99% reduction of the universe of all available configurations. Energy savings of up to 59.77%, 61.38% and 17.7% were observed when compared to the performance, ondemand and powersave Linux governors, respectively, with higher or similar performance

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Pooled analysis of WHO Surgical Safety Checklist use and mortality after emergency laparotomy

Background The World Health Organization (WHO) Surgical Safety Checklist has fostered safe practice for 10 years, yet its place in emergency surgery has not been assessed on a global scale. The aim of this study was to evaluate reported checklist use in emergency settings and examine the relationship with perioperative mortality in patients who had emergency laparotomy. Methods In two multinational cohort studies, adults undergoing emergency laparotomy were compared with those having elective gastrointestinal surgery. Relationships between reported checklist use and mortality were determined using multivariable logistic regression and bootstrapped simulation. Results Of 12 296 patients included from 76 countries, 4843 underwent emergency laparotomy. After adjusting for patient and disease factors, checklist use before emergency laparotomy was more common in countries with a high Human Development Index (HDI) (2455 of 2741, 89.6 per cent) compared with that in countries with a middle (753 of 1242, 60.6 per cent; odds ratio (OR) 0.17, 95 per cent c.i. 0.14 to 0.21, P <0001) or low (363 of 860, 422 per cent; OR 008, 007 to 010, P <0.001) HDI. Checklist use was less common in elective surgery than for emergency laparotomy in high-HDI countries (risk difference -94 (95 per cent c.i. -11.9 to -6.9) per cent; P <0001), but the relationship was reversed in low-HDI countries (+121 (+7.0 to +173) per cent; P <0001). In multivariable models, checklist use was associated with a lower 30-day perioperative mortality (OR 0.60, 0.50 to 073; P <0.001). The greatest absolute benefit was seen for emergency surgery in low- and middle-HDI countries. Conclusion Checklist use in emergency laparotomy was associated with a significantly lower perioperative mortality rate. Checklist use in low-HDI countries was half that in high-HDI countries.Peer reviewe

Aurora: Otimização Transparente de Aplicações OpenMP

Efficiently exploiting thread-level parallelism has been challenging for software developers. As many parallel applications do not scale with the number of cores, blindly increasing the number of threads may not produce the best results in performance or energy. However, the task of rightly choosing the ideal amount of threads is not straightforward: many variables are involved (e.g. off-chip bus saturation and overhead of datasynchronization), which will change according to different aspects of the system at hand (e.g., input set, micro-architecture) and even during execution. To address this complex scenario, this thesis presents Aurora. It is capable of automatically finding, at run-time and with minimum overhead, the optimal number of threads for each parallel region of the application and re-adapt in cases the behavior of a region changes during execution. Aurora works with OpenMP and is completely transparent to both designer and end-user: given an OpenMP application binary, Aurora optimizes it without any code transformation or recompilation. By executing fifteen well-known benchmarks on four multi-core processors, Aurora improves the trade-off between performance and energy by up to: 98% over the standard OpenMP execution; 86% over the built-in feature of OpenMP that dynamically adjusts the number of threads; and 91% over a feedback-driven threading emulation.A exploração eficiente do paralelismo no nível de threads tem sido um desafio para os desenvolvedores de softwares. Como muitas aplicações não escalam com o número de núcleos, aumentar cegamente o número de threads pode não produzir os melhores resultados em desempenho ou energia. No entanto, a tarefa de escolher corretamente o número ideal de threads não é simples: muitas variáveis estão envolvidas (por exemplo, saturação do barramento off-chip e sobrecarga de sincronização de dados), que mudam de acordo com diferentes aspectos do sistema (por exemplo, conjunto de entrada, micro-arquitetura) e mesmo durante a execução da aplicação. Para abordar esse complexo cenário, esta tese apresenta Aurora. Ela é capaz de encontrar automaticamente, em tempo de execução e com o mínimo de sobrecarga, o número ideal de threads para cada região paralela da aplicação e se readaptar nos casos em que o comportamento de uma região muda durante a execução. Aurora trabalha com o OpenMP e é completamente transparente tanto para o programador quanto para o usuário final: dado um binário de uma aplicação OpenMP, Aurora o otimiza sem nenhuma transformação ou recompilação de código. Através da execução de quinze benchmarks conhecidos em quatro processadores multi-core, mostramos que Aurora melhora o trade-off entre desempenho e energia em até: 98% sobre a execução padrão do OpenMP; 86% sobre o recurso interno do OpenMP que ajusta dinamicamente o número de threads; e 91% quando comparado a uma emulação do feedback-driven threading

Avaliação do desempenho e consumo energético de diferentes interfaces de programação paralela em sistemas embarcados e de propósito geral

Nos sistemas computacionais atuais, enquanto é necessário explorar a disponibilidade de múltiplos núcleos, também é obrigatório consumir menos energia. Para acelerar o processo de desenvolvimento de aplicações paralelas e o tornar mais transparente ao programador, Interfaces de Programação Paralela (IPPs) são largamente utilizadas. Entretanto, cada IPP implementa diferentes formas para trocar dados usando regiões compartilhadas da memória. Estas regiões são, geralmente, mais distantes do processador do que regiões privadas da memória e, por consequência, possuem maior tempo de acesso e consumo de energia. Ademais, o sistema de memória dos processadores embarcados é diferente em hierarquia, tamanho, tempo de acesso, consumo de energia, etc., quando comparado aos processadores de propósito geral. Assim, considerando o cenário supracitado, com diferentes IPPs sendo utilizadas em sistemas multicore com diferentes requisitos, neste trabalho será mostrado que cada interface possui comportamento diferente em termos de desempenho, consumo de energia e Energy-Delay Product (EDP), e que este comportamento varia de acordo com a característica da aplicação e o processador utilizado (propósito geral ou embarcado). Por exemplo, Pthreads consome 8% menos energia que o melhor caso de OpenMP; 12% menos que MPI-1; e 8% menos que MPI-2, considerando todos os benchmarks no processador Intel Core i7 (propósito geral). Em contrapartida, no processador ARM Cortex-A9 (sistema embarcado), o melhor caso com OpenMP consumiu 2% menos energia que Pthreads; 6% menos que MPI-1; e 15% menos que MPI-2, para o mesmo conjunto de benchmarks.In current computer systems, while it is necessary to exploit the availability of multiple cores, it is also mandatory to consume less energy. To accelerate the development of parallel applications and to make it more transparent to the programmer, Parallel APIs (Application Programming Interfaces) are widely used. However, each Parallel API implements different ways to exchange data using shared memory regions. These regions are generally more remote than the private ones, and therefore have greater access time and energy consumption. Furthermore, the memory system of embedded processors is different with regard to hierarchy, size, access time, energy consumption, etc., when compared to general purpose processors. Thus, considering the above scenario, with different Parallel APIs being used in multicore systems with different requirements, this work will show that each interface has different behavior in terms of performance, energy consumption and Energy-Delay Product (EDP), and that this behavior varies according to the characteristic of the application and the processor employed (general purpose or embedded). For example, as a result of this work, we have observed that Pthreads consumes 8% less energy than the best case of OpenMP; 12% less than MPI-1; and 8% less than MPI-2, considering all benchmarks on the Intel Core i7 (general purpose). In contrast, in the ARM Cortex-A9 processor (embedded system), the best case with OpenMP consumed 2% less energy than Pthreads; 6% less than MPI-1; and 15% less than MPI-2 for the same benchmarks set

Avaliação do desempenho e consumo energético de diferentes interfaces de programação paralela em sistemas embarcados e de propósito geral

Nos sistemas computacionais atuais, enquanto é necessário explorar a disponibilidade de múltiplos núcleos, também é obrigatório consumir menos energia. Para acelerar o processo de desenvolvimento de aplicações paralelas e o tornar mais transparente ao programador, Interfaces de Programação Paralela (IPPs) são largamente utilizadas. Entretanto, cada IPP implementa diferentes formas para trocar dados usando regiões compartilhadas da memória. Estas regiões são, geralmente, mais distantes do processador do que regiões privadas da memória e, por consequência, possuem maior tempo de acesso e consumo de energia. Ademais, o sistema de memória dos processadores embarcados é diferente em hierarquia, tamanho, tempo de acesso, consumo de energia, etc., quando comparado aos processadores de propósito geral. Assim, considerando o cenário supracitado, com diferentes IPPs sendo utilizadas em sistemas multicore com diferentes requisitos, neste trabalho será mostrado que cada interface possui comportamento diferente em termos de desempenho, consumo de energia e Energy-Delay Product (EDP), e que este comportamento varia de acordo com a característica da aplicação e o processador utilizado (propósito geral ou embarcado). Por exemplo, Pthreads consome 8% menos energia que o melhor caso de OpenMP; 12% menos que MPI-1; e 8% menos que MPI-2, considerando todos os benchmarks no processador Intel Core i7 (propósito geral). Em contrapartida, no processador ARM Cortex-A9 (sistema embarcado), o melhor caso com OpenMP consumiu 2% menos energia que Pthreads; 6% menos que MPI-1; e 15% menos que MPI-2, para o mesmo conjunto de benchmarks.In current computer systems, while it is necessary to exploit the availability of multiple cores, it is also mandatory to consume less energy. To accelerate the development of parallel applications and to make it more transparent to the programmer, Parallel APIs (Application Programming Interfaces) are widely used. However, each Parallel API implements different ways to exchange data using shared memory regions. These regions are generally more remote than the private ones, and therefore have greater access time and energy consumption. Furthermore, the memory system of embedded processors is different with regard to hierarchy, size, access time, energy consumption, etc., when compared to general purpose processors. Thus, considering the above scenario, with different Parallel APIs being used in multicore systems with different requirements, this work will show that each interface has different behavior in terms of performance, energy consumption and Energy-Delay Product (EDP), and that this behavior varies according to the characteristic of the application and the processor employed (general purpose or embedded). For example, as a result of this work, we have observed that Pthreads consumes 8% less energy than the best case of OpenMP; 12% less than MPI-1; and 8% less than MPI-2, considering all benchmarks on the Intel Core i7 (general purpose). In contrast, in the ARM Cortex-A9 processor (embedded system), the best case with OpenMP consumed 2% less energy than Pthreads; 6% less than MPI-1; and 15% less than MPI-2 for the same benchmarks set