P-SOCRATES: A parallel software framework for time-critical many-core systems

Article in Press, Corrected Proof

Towards the Combination of Work-Stealing and Semi-Partitioned Scheduling for Parallel Tasks

Paper/Poster presented in Work in Progress Session, 28th GI/ITG International Conference on Architecture of Computing Systems (ARCS 2015). 24 to 26, Mar, 2015. Porto, Portugal.

Towards the Combination of Work-Stealing and Semi-Partitioned Scheduling for Parallel Tasks

Poster presented in Work in Progress Session, 28th GI/ITG International Conference on Architecture of Computing Systems (ARCS 2015). 24 to 26, Mar, 2015. Porto, Portugal.

Detection of Trypanosoma cruzi and Trypanosoma rangeli infection in triatomine vectors by amplification of the histone H2A/SIRE and the sno-RNA-C11 genes

Trypanosoma rangeli is non pathogenic for humans but of important medical and epidemiological interest because it shares vertebrate hosts, insect vectors, reservoirs and geographic areas with T. cruzi, the etiological agent of Chagas disease. Therefore, in this work, we set up two PCR reactions, TcH2AF/R and TrFR2, to distinguish T. cruzi from T. rangeli in mixed infections of vectors based on amplification of the histone H2A/SIRE and the small nucleolar RNA Cl1 genes, respectively. Both PCRs were able to appropriately detect all T. cruzi or T. rangeli experimentally infected-triatomines, as well as the S35/S36 PCR which amplifies the variable region of minicircle kDNA of T. cruzi. In mixed infections, whereas T. cruzi DNA was amplified in 100% of samples with TcH2AF/R and S35/S36 PCRs, T. rangeli was detected in 71% with TrF/R2 and in 6% with S35/S36. In a group of Rhodnius colombiensis collected from Coyaima (Colombia), T. cruzi was identified in 100% with both PCRs and T. rangeli in 14% with TrF/R2 and 10% with S35/S36 PCR. These results show that TcH2AF/R and TrF/R2 PCRs which are capable of recognizing all T. cruzi and T. rangeli strains and lineages could be useful for diagnosis as well as for epidemiological field studies of T. cruzi and T. rangeli vector infections.

Real-time Parallel Applications on Many-core Architectures

Presented at INForum - Simpósio de Informática (INFORUM 2015). 7 to 8, Sep, 2015. Portugal.

Parallel Software framework for time-critical many-core systems

The recent technological advancements and market trends are causing an interesting phenomenon towards the convergence of High-Performance Computing (HPC) and Embedded Computing (EC) domains. On one side, new kinds of HPC applications are being required by markets needing huge amounts of information to be processed within a bounded amount of time. On the other side, EC systems are increasingly concerned with providing higher performance in real-time, challenging the performance capabilities of current architectures. The advent of next-generation many-core embedded platforms has the chance of intercepting this converging need for predictable high-performance, allowing HPC and EC applications to be executed on efficient and powerful heterogeneous architectures integrating general-purpose processors with many-core computing fabrics. To this end, it is of paramount importance to develop new techniques for exploiting the massively parallel computation capabilities of such platforms in a predictable way. P-SOCRATES will tackle this important challenge by merging leading research groups from the HPC and EC communities. The time-criticality and parallelisation challenges common to both areas will be addressed by proposing an integrated framework for executing workload-intensive applications with real-time requirements on top of next-generation commercial-off-the-shelf (COTS) platforms based on many-core accelerated architectures. The project will investigate new HPC techniques that fulfil real-time requirements. The main sources of indeterminism will be identified, proposing efficient mapping and scheduling algorithms, along with the associated timing and schedulability analysis, to guarantee the real-time and performance requirements of the applications.

Epidemiological and ecological aspects related to malaria in the area of influence of the lake at Porto Primavera dam, in western São Paulo State, Brazil

A study was carried out in the area of influence of the Porto Primavera Hydroelectric Power Station, in western São Paulo State, to investigate ecological and epidemiological aspects of malaria in the area and monitor the profile of the anopheline populations following the environmental changes brought about by the construction of the lake. Mosquitoes captured were analyzed by standardized indicator species analysis (ISA) before and during different flooding phases (253 m and 257 m elevations). The local human population was studied by means of parasitological (thin/thick blood smears), molecular (PCR) and serological tests. Serological tests consisted of Enzyme Linked Immunosorbent Assay (ELISA) with synthetic peptides of the circumsporozoite protein (CSP) from classic Plasmodium vivax, P. vivax variants (VK247 and "vivax-like"), P. malariae and P. falciparum and Indirect Immunofluorescence Assay (IFA) with asexual forms of P. vivax, P. malariae and P. falciparum. The results of the entomological survey indicated that, although the Anopheles darlingi population increased after the flooding, the population density remained very low. No malaria, parasite infection or DNA was detected in the inhabitants of the study area. However, there was a low frequency of antibodies against asexual forms and a significant prevalence of antibodies against P. vivax, P. vivax variants, P. falciparum and P. malariae; the presence of these antibodies may result from recent or less recent contact with human or simian Plasmodium (a parallel study in the same area revealed the existence of a sylvatic cycle). Nevertheless, these results suggest that, as in other places where malaria is present and potential vectors circulate, the local epidemiological conditions observed could potentially support the transmission of malaria in Porto Primavera Lake if infected individuals are introduced in sufficient numbers. Further studies are required to elucidate the phenomena described in this paper.

Parallel run-time for CO-OPN

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Parallel programming in biomedical signal processing

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Multicore Scheduling of Real-Time Irregular Parallel Algorithms in Linux

Face à estagnação da tecnologia uniprocessador registada na passada década, aos principais fabricantes de microprocessadores encontraram na tecnologia multi-core a resposta `as crescentes necessidades de processamento do mercado. Durante anos, os desenvolvedores de software viram as suas aplicações acompanhar os ganhos de performance conferidos por cada nova geração de processadores sequenciais, mas `a medida que a capacidade de processamento escala em função do número de processadores, a computação sequencial tem de ser decomposta em várias partes concorrentes que possam executar em paralelo, para que possam utilizar as unidades de processamento adicionais e completar mais rapidamente. A programação paralela implica um paradigma completamente distinto da programação sequencial. Ao contrário dos computadores sequenciais tipificados no modelo de Von Neumann, a heterogeneidade de arquiteturas paralelas requer modelos de programação paralela que abstraiam os programadores dos detalhes da arquitectura e simplifiquem o desenvolvimento de aplicações concorrentes. Os modelos de programação paralela mais populares incitam os programadores a identificar instruções concorrentes na sua lógica de programação, e a especificá-las sob a forma de tarefas que possam ser atribuídas a processadores distintos para executarem em simultâneo. Estas tarefas são tipicamente lançadas durante a execução, e atribuídas aos processadores pelo motor de execução subjacente. Como os requisitos de processamento costumam ser variáveis, e não são conhecidos a priori, o mapeamento de tarefas para processadores tem de ser determinado dinamicamente, em resposta a alterações imprevisíveis dos requisitos de execução. `A medida que o volume da computação cresce, torna-se cada vez menos viável garantir as suas restrições temporais em plataformas uniprocessador. Enquanto os sistemas de tempo real se começam a adaptar ao paradigma de computação paralela, há uma crescente aposta em integrar execuções de tempo real com aplicações interativas no mesmo hardware, num mundo em que a tecnologia se torna cada vez mais pequena, leve, ubíqua, e portável. Esta integração requer soluções de escalonamento que simultaneamente garantam os requisitos temporais das tarefas de tempo real e mantenham um nível aceitável de QoS para as restantes execuções. Para tal, torna-se imperativo que as aplicações de tempo real paralelizem, de forma a minimizar os seus tempos de resposta e maximizar a utilização dos recursos de processamento. Isto introduz uma nova dimensão ao problema do escalonamento, que tem de responder de forma correcta a novos requisitos de execução imprevisíveis e rapidamente conjeturar o mapeamento de tarefas que melhor beneficie os critérios de performance do sistema. A técnica de escalonamento baseado em servidores permite reservar uma fração da capacidade de processamento para a execução de tarefas de tempo real, e assegurar que os efeitos de latência na sua execução não afectam as reservas estipuladas para outras execuções. No caso de tarefas escalonadas pelo tempo de execução máximo, ou tarefas com tempos de execução variáveis, torna-se provável que a largura de banda estipulada não seja consumida por completo. Para melhorar a utilização do sistema, os algoritmos de partilha de largura de banda (capacity-sharing) doam a capacidade não utilizada para a execução de outras tarefas, mantendo as garantias de isolamento entre servidores. Com eficiência comprovada em termos de espaço, tempo, e comunicação, o mecanismo de work-stealing tem vindo a ganhar popularidade como metodologia para o escalonamento de tarefas com paralelismo dinâmico e irregular. O algoritmo p-CSWS combina escalonamento baseado em servidores com capacity-sharing e work-stealing para cobrir as necessidades de escalonamento dos sistemas abertos de tempo real. Enquanto o escalonamento em servidores permite partilhar os recursos de processamento sem interferências a nível dos atrasos, uma nova política de work-stealing que opera sobre o mecanismo de capacity-sharing aplica uma exploração de paralelismo que melhora os tempos de resposta das aplicações e melhora a utilização do sistema. Esta tese propõe uma implementação do algoritmo p-CSWS para o Linux. Em concordância com a estrutura modular do escalonador do Linux, ´e definida uma nova classe de escalonamento que visa avaliar a aplicabilidade da heurística p-CSWS em circunstâncias reais. Ultrapassados os obstáculos intrínsecos `a programação da kernel do Linux, os extensos testes experimentais provam que o p-CSWS ´e mais do que um conceito teórico atrativo, e que a exploração heurística de paralelismo proposta pelo algoritmo beneficia os tempos de resposta das aplicações de tempo real, bem como a performance e eficiência da plataforma multiprocessador.

SEASONAL DISTRIBUTION OF MALARIA VECTORS (DIPTERA: CULICIDAE) IN RURAL LOCALITIES OF PORTO VELHO, RONDÔNIA, BRAZILIAN AMAZON

We conducted a survey of the malaria vectors in an area where a power line had been constructed, between the municipalities of Porto Velho and Rio Branco, in the states of Rondônia and Acre, respectively. The present paper relates to the results of the survey of Anopheles fauna conducted in the state of Rondônia. Mosquito field collections were performed in six villages along the federal highway BR 364 in the municipality of Porto Velho, namely Porto Velho, Jaci Paraná, Mutum Paraná, Vila Abunã, Vista Alegre do Abunã, and Extrema. Mosquito captures were performed at three distinct sites in each locality during the months of February, July, and October 2011 using a protected human-landing catch method; outdoor and indoor captures were conducted simultaneously at each site for six hours. In the six sampled areas, we captured 2,185 mosquitoes belonging to seven Anopheles species. Of these specimens, 95.1% consisted of Anopheles darlingi, 1.8% An. triannulatus l.s., 1.7% An. deaneorum, 0.8% An. konderi l.s., 0.4 An. braziliensis, 0.1% An. albitarsis l.s., and 0.1% An. benarrochi. An. darlingi was the only species found in all localities; the remaining species occurred in sites with specific characteristics.

EVALUATION OF SUBLETHAL EFFECTS OF Ipomoea cairica LINN. EXTRACT ON LIFE HISTORY TRAITS OF DENGUE VECTORS

Plant derived insecticides have considerable potential for mosquito control because these products are safer than conventional insecticides. This study aimed to investigate sublethal activities of Ipomoea carica or railway creeper crude acethonilic extract against life history trait of dengue vectors, Aedes albopictus and Aedes aegypti. The late third instar larvae of Ae. albopictus and Ae. aegypti were exposed to a sublethal dose at LC50 and larvae that survived were further cultured. Overall, Ipomea cairica crude extracts affected the whole life history of both Aedes species. The study demonstrated significantly lower egg production (fecundity) and eggs hatchability (fertility) in Ae. albopictus. The sublethal dose of crude extracts reduced significantly the width of larval head capsule and the wing length of both sexes in both Aedes species. The significance of sublethal effects of I. cairica against Aedes mosquitoes was an additional hallmark to demonstrate further activity of this plant despite its direct toxicity to the larvae. The reduced reproductive capacity as well as morphological and physiological anomalies are some of the effects that make I. cairica a potential candidate to be used as a new plant-based insecticide to control dengue vectors.

Pathogenicity of Evlachovaea sp (Hyphomycetes), a new species isolated from Triatoma sordida, in Chagas' disease vectors

Evlachovaea sp was tested on nymphs of 5 Triatoma spp 5 Rhodnius spp, Panstrongylus herreri and Dipetalogaster maximus at 25°C, 75% humidity and humidity >98%. Most species showed susceptibility to fungal infection at high humidity. Mortality was reduced at 75% humidity. Fungal development was observed on 69.5% of cadavers.

A system’s approach to cache hierarchy-aware decomposition of data-parallel computations

Dissertação para obtenção do Grau de Mestre em Engenharia Informática