Sporadic multiprocessor scheduling with few preemptions

Consider the problem of scheduling n sporadic tasks so as to meet deadlines on m identical processors. A task is characterised by its minimum interarrival time and its worst-case execution time. Tasks are preemptible and may migrate between processors. We propose an algorithm with limited migration, configurable for a utilisation bound of 88% with few preemptions (and arbitrarily close to 100% with more preemptions).

Scheduling arbitrary-deadline sporadic task systems on multiprocessors

A new algorithm is proposed for scheduling preemptible arbitrary-deadline sporadic task systems upon multiprocessor platforms, with interprocessor migration permitted. This algorithm is based on a task-splitting approach - while most tasks are entirely assigned to specific processors, a few tasks (fewer than the number of processors) may be split across two processors. This algorithm can be used for two distinct purposes: for actually scheduling specific sporadic task systems, and for feasibility analysis. Simulation- based evaluation indicates that this algorithm offers a significant improvement on the ability to schedule arbitrary- deadline sporadic task systems as compared to the contemporary state-of-art. With regard to feasibility analysis, the new algorithm is proved to offer superior performance guarantees in comparison to prior feasibility tests.

The utilization bound of static-priority preemptive partitioned multiprocessor scheduling is 50%

This paper studies static-priority preemptive scheduling on a multiprocessor using partitioned scheduling. We propose a new scheduling algorithm and prove that if the proposed algorithm is used and if less than 50% of the capacity is requested then all deadlines are met. It is known that for every static-priority multiprocessor scheduling algorithm, there is a task set that misses a deadline although the requested capacity is arbitrary close to 50%.

Multiprocessor scheduling with few preemptions

Consider the problem of scheduling a set of periodically arriving tasks on a multiprocessor with the goal of meeting deadlines. Processors are identical and have the same speed. Tasks can be preempted and they can migrate between processors. We propose an algorithm with a utilization bound of 66% and with few preemptions. It can trade a higher utilization bound for more preemption and in doing so it has a utilization bound of 100%.

Real-time scheduling with resource sharing on heterogeneous multiprocessors

Consider the problem of scheduling a task set τ of implicit-deadline sporadic tasks to meet all deadlines on a t-type heterogeneous multiprocessor platform where tasks may access multiple shared resources. The multiprocessor platform has m k processors of type-k, where k∈{1,2,…,t}. The execution time of a task depends on the type of processor on which it executes. The set of shared resources is denoted by R. For each task τ i , there is a resource set R i ⊆R such that for each job of τ i , during one phase of its execution, the job requests to hold the resource set R i exclusively with the interpretation that (i) the job makes a single request to hold all the resources in the resource set R i and (ii) at all times, when a job of τ i holds R i , no other job holds any resource in R i . Each job of task τ i may request the resource set R i at most once during its execution. A job is allowed to migrate when it requests a resource set and when it releases the resource set but a job is not allowed to migrate at other times. Our goal is to design a scheduling algorithm for this problem and prove its performance. We propose an algorithm, LP-EE-vpr, which offers the guarantee that if an implicit-deadline sporadic task set is schedulable on a t-type heterogeneous multiprocessor platform by an optimal scheduling algorithm that allows a job to migrate only when it requests or releases a resource set, then our algorithm also meets the deadlines with the same restriction on job migration, if given processors 4×(1+MAXP×⌈|P|×MAXPmin{m1,m2,…,mt}⌉) times as fast. (Here MAXP and |P| are computed based on the resource sets that tasks request.) For the special case that each task requests at most one resource, the bound of LP-EE-vpr collapses to 4×(1+⌈|R|min{m1,m2,…,mt}⌉). To the best of our knowledge, LP-EE-vpr is the first algorithm with proven performance guarantee for real-time scheduling of sporadic tasks with resource sharing on t-type heterogeneous multiprocessors.

Localization system for pedestrians based on sensor and information fusion

Nowadays there is an increase of location-aware mobile applications. However, these applications only retrieve location with a mobile device's GPS chip. This means that in indoor or in more dense environments these applications don't work properly. To provide location information everywhere a pedestrian Inertial Navigation System (INS) is typically used, but these systems can have a large estimation error since, in order to turn the system wearable, they use low-cost and low-power sensors. In this work a pedestrian INS is proposed, where force sensors were included to combine with the accelerometer data in order to have a better detection of the stance phase of the human gait cycle, which leads to improvements in location estimation. Besides sensor fusion an information fusion architecture is proposed, based on the information from GPS and several inertial units placed on the pedestrian body, that will be used to learn the pedestrian gait behavior to correct, in real-time, the inertial sensors errors, thus improving location estimation.

Global and Partitioned Multiprocessor Fixed Priority Scheduling with Deferred Pre-emption

This article introduces schedulability analysis for global fixed priority scheduling with deferred preemption (gFPDS) for homogeneous multiprocessor systems. gFPDS is a superset of global fixed priority pre-emptive scheduling (gFPPS) and global fixed priority non-pre-emptive scheduling (gFPNS). We show how schedulability can be improved using gFPDS via appropriate choice of priority assignment and final non-pre-emptive region lengths, and provide algorithms which optimize schedulability in this way. Via an experimental evaluation we compare the performance of multiprocessor scheduling using global approaches: gFPDS, gFPPS, and gFPNS, and also partitioned approaches employing FPDS, FPPS, and FPNS on each processor.

Considerations on the Least Upper Bound for Mixed-Criticality Real-Time Systems

5th Brazilian Symposium on Computing Systems Engineering, SBESC 2015 (SBESC 2015). 3 to 6, Nov, 2015. Foz do Iguaçu, Brasil.

Hard real-time multiprocessor scheduling resilient to core failures

Presented at 21st IEEE International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA 2015). 19 to 21, Aug, 2015, pp 122-131. Hong Kong, China.

Real-time Task-Splitting scheduling algorithms framework

Nos dias de hoje, os sistemas de tempo real crescem em importância e complexidade. Mediante a passagem do ambiente uniprocessador para multiprocessador, o trabalho realizado no primeiro não é completamente aplicável no segundo, dado que o nível de complexidade difere, principalmente devido à existência de múltiplos processadores no sistema. Cedo percebeu-se, que a complexidade do problema não cresce linearmente com a adição destes. Na verdade, esta complexidade apresenta-se como uma barreira ao avanço científico nesta área que, para já, se mantém desconhecida, e isto testemunha-se, essencialmente no caso de escalonamento de tarefas. A passagem para este novo ambiente, quer se trate de sistemas de tempo real ou não, promete gerar a oportunidade de realizar trabalho que no primeiro caso nunca seria possível, criando assim, novas garantias de desempenho, menos gastos monetários e menores consumos de energia. Este último fator, apresentou-se desde cedo, como, talvez, a maior barreira de desenvolvimento de novos processadores na área uniprocessador, dado que, à medida que novos eram lançados para o mercado, ao mesmo tempo que ofereciam maior performance, foram levando ao conhecimento de um limite de geração de calor que obrigou ao surgimento da área multiprocessador. No futuro, espera-se que o número de processadores num determinado chip venha a aumentar, e como é óbvio, novas técnicas de exploração das suas inerentes vantagens têm de ser desenvolvidas, e a área relacionada com os algoritmos de escalonamento não é exceção. Ao longo dos anos, diferentes categorias de algoritmos multiprocessador para dar resposta a este problema têm vindo a ser desenvolvidos, destacando-se principalmente estes: globais, particionados e semi-particionados. A perspectiva global, supõe a existência de uma fila global que é acessível por todos os processadores disponíveis. Este fato torna disponível a migração de tarefas, isto é, é possível parar a execução de uma tarefa e resumir a sua execução num processador distinto. Num dado instante, num grupo de tarefas, m, as tarefas de maior prioridade são selecionadas para execução. Este tipo promete limites de utilização altos, a custo elevado de preempções/migrações de tarefas. Em contraste, os algoritmos particionados, colocam as tarefas em partições, e estas, são atribuídas a um dos processadores disponíveis, isto é, para cada processador, é atribuída uma partição. Por essa razão, a migração de tarefas não é possível, acabando por fazer com que o limite de utilização não seja tão alto quando comparado com o caso anterior, mas o número de preempções de tarefas decresce significativamente. O esquema semi-particionado, é uma resposta de caráter hibrido entre os casos anteriores, pois existem tarefas que são particionadas, para serem executadas exclusivamente por um grupo de processadores, e outras que são atribuídas a apenas um processador. Com isto, resulta uma solução que é capaz de distribuir o trabalho a ser realizado de uma forma mais eficiente e balanceada. Infelizmente, para todos estes casos, existe uma discrepância entre a teoria e a prática, pois acaba-se por se assumir conceitos que não são aplicáveis na vida real. Para dar resposta a este problema, é necessário implementar estes algoritmos de escalonamento em sistemas operativos reais e averiguar a sua aplicabilidade, para caso isso não aconteça, as alterações necessárias sejam feitas, quer a nível teórico quer a nível prá

Design and analysis of ChIP-Seq experiments for nuclear factor I DNA-binding proteins

SUMMARY : Eukaryotic DNA interacts with the nuclear proteins using non-covalent ionic interactions. Proteins can recognize specific nucleotide sequences based on the sterical interactions with the DNA and these specific protein-DNA interactions are the basis for many nuclear processes, e.g. gene transcription, chromosomal replication, and recombination. New technology termed ChIP-Seq has been recently developed for the analysis of protein-DNA interactions on a whole genome scale and it is based on immunoprecipitation of chromatin and high-throughput DNA sequencing procedure. ChIP-Seq is a novel technique with a great potential to replace older techniques for mapping of protein-DNA interactions. In this thesis, we bring some new insights into the ChIP-Seq data analysis. First, we point out to some common and so far unknown artifacts of the method. Sequence tag distribution in the genome does not follow uniform distribution and we have found extreme hot-spots of tag accumulation over specific loci in the human and mouse genomes. These artifactual sequence tags accumulations will create false peaks in every ChIP-Seq dataset and we propose different filtering methods to reduce the number of false positives. Next, we propose random sampling as a powerful analytical tool in the ChIP-Seq data analysis that could be used to infer biological knowledge from the massive ChIP-Seq datasets. We created unbiased random sampling algorithm and we used this methodology to reveal some of the important biological properties of Nuclear Factor I DNA binding proteins. Finally, by analyzing the ChIP-Seq data in detail, we revealed that Nuclear Factor I transcription factors mainly act as activators of transcription, and that they are associated with specific chromatin modifications that are markers of open chromatin. We speculate that NFI factors only interact with the DNA wrapped around the nucleosome. We also found multiple loci that indicate possible chromatin barrier activity of NFI proteins, which could suggest the use of NFI binding sequences as chromatin insulators in biotechnology applications. RESUME : L'ADN des eucaryotes interagit avec les protéines nucléaires par des interactions noncovalentes ioniques. Les protéines peuvent reconnaître les séquences nucléotidiques spécifiques basées sur l'interaction stérique avec l'ADN, et des interactions spécifiques contrôlent de nombreux processus nucléaire, p.ex. transcription du gène, la réplication chromosomique, et la recombinaison. Une nouvelle technologie appelée ChIP-Seq a été récemment développée pour l'analyse des interactions protéine-ADN à l'échelle du génome entier et cette approche est basée sur l'immuno-précipitation de la chromatine et sur la procédure de séquençage de l'ADN à haut débit. La nouvelle approche ChIP-Seq a donc un fort potentiel pour remplacer les anciennes techniques de cartographie des interactions protéine-ADN. Dans cette thèse, nous apportons de nouvelles perspectives dans l'analyse des données ChIP-Seq. Tout d'abord, nous avons identifié des artefacts très communs associés à cette méthode qui étaient jusqu'à présent insoupçonnés. La distribution des séquences dans le génome ne suit pas une distribution uniforme et nous avons constaté des positions extrêmes d'accumulation de séquence à des régions spécifiques, des génomes humains et de la souris. Ces accumulations des séquences artéfactuelles créera de faux pics dans toutes les données ChIP-Seq, et nous proposons différentes méthodes de filtrage pour réduire le nombre de faux positifs. Ensuite, nous proposons un nouvel échantillonnage aléatoire comme un outil puissant d'analyse des données ChIP-Seq, ce qui pourraient augmenter l'acquisition de connaissances biologiques à partir des données ChIP-Seq. Nous avons créé un algorithme d'échantillonnage aléatoire et nous avons utilisé cette méthode pour révéler certaines des propriétés biologiques importantes de protéines liant à l'ADN nommés Facteur Nucléaire I (NFI). Enfin, en analysant en détail les données de ChIP-Seq pour la famille de facteurs de transcription nommés Facteur Nucléaire I, nous avons révélé que ces protéines agissent principalement comme des activateurs de transcription, et qu'elles sont associées à des modifications de la chromatine spécifiques qui sont des marqueurs de la chromatine ouverte. Nous pensons que lés facteurs NFI interagir uniquement avec l'ADN enroulé autour du nucléosome. Nous avons également constaté plusieurs régions génomiques qui indiquent une éventuelle activité de barrière chromatinienne des protéines NFI, ce qui pourrait suggérer l'utilisation de séquences de liaison NFI comme séquences isolatrices dans des applications de la biotechnologie.

Exploring Cross-layer power management for PGAS applications on the SCC platform

Technological limitations and power constraints are resulting in high-performance parallel computing architectures that are based on large numbers of high-core-count processors. Commercially available processors are now at 8 and 16 cores and experimental platforms, such as the many-core Intel Single-chip Cloud Computer (SCC) platform, provide much higher core counts. These trends are presenting new sets of challenges to HPC applications including programming complexity and the need for extreme energy efficiency.In this work, we first investigate the power behavior of scientific PGAS application kernels on the SCC platform, and explore opportunities and challenges for power management within the PGAS framework. Results obtained via empirical evaluation of Unified Parallel C (UPC) applications on the SCC platform under different constraints, show that, for specific operations, the potential for energy savings in PGAS is large; and power/performance trade-offs can be effectively managed using a cross-layerapproach. We investigate cross-layer power management using PGAS language extensions and runtime mechanisms that manipulate power/performance tradeoffs. Specifically, we present the design, implementation and evaluation of such a middleware for application-aware cross-layer power management of UPC applications on the SCC platform. Finally, based on our observations, we provide a set of recommendations and insights that can be used to support similar power management for PGAS applications on other many-core platforms.

The joint R&D project: The case of the first Brazilian microcontroller chip

ABSTRACT The interorganizational cooperation, through joint efforts with various actors, allows the high-tech companies to complement resources, especially in R&D projects. Collaborative projects have been identified in many studies as an important strategy to produce complex products and services in uncertain and competitive environments. Thus, this research aims at deepening the understanding of how the development dynamics of a collaborative R&D project in an industry of high technology occur. In order to achieve the proposed objective, the R&D project of the first microcontroller in the Brazilian semiconductor industry was defined as the object of analysis. The empirical choice is justified by the uniqueness of the case, besides bringing a diversity of actors and a level of complementarity of resources that were significant to the success of the project. Given the motivation to know who the actors were and what the main forms of interorganizational coordination were used in this project, interviews were carried out and a questionnaire was also made, besides other documents related to the project. The results presented show a network of nine actors and their roles in the interorganizational collaboration process, as well as the forms of social and temporal overlapping, used in the coordination of collective efforts. Focusing on the mechanisms of temporal and social integration highlighted throughout the study, the inclusion of R&D projects in the typology for interorganizational projects is proposed in this paper, which was also proposed by Jones and Lichtenstein (2008).

Nanomotors: new strategies of (bio)sensing based on motion

Nanomotors are nanoscale devices capable of converting energy into movement and forces. Among them, self-propelled nanomotors offer considerable promise for developing new and novel bioanalytical and biosensing strategies based on the direct isolation of target biomolecules or changes in their movement in the presence of target analytes. The mainachievements of this project consists on the development of receptor-functionalized nanomotors that offer direct and rapid target detection, isolation and transport from raw biological samples without preparatory and washing steps. For example, microtube engines functionalized with aptamer, antibody, lectin and enzymes receptors were used for the direct isolation of analytes of biomedical interest, including proteins and whole cells, among others. A target protein was also isolated from a complex sample by using an antigen-functionalized microengine navigating into the reservoirs of a lab-on-a-chip device. The new nanomotorbased target biomarkers detection strategy not only offers highly sensitive, rapid, simple and low cost alternative for the isolation and transport of target molecules, but also represents a new dimension of analytical information based on motion. The recognition events can be easily visualized by optical microscope (without any sophisticated analytical instrument) to reveal the target presence and concentration. The use of artificial nanomachines has shown not only to be useful for (bio)recognition and (bio)transport but also for detection of environmental contamination and remediation. In this context, micromotors modified with superhydrophobic layer demonstrated that effectively interacted, captured, transported and removed oil droplets from oil contaminated samples. Finally, a unique micromotor-based strategy for water-quality testing, that mimics live-fish water-quality testing, based on changes in the propulsion behavior of artificial biocatalytic microswimmers in the presence of aquatic pollutants was also developed. The attractive features of the new micromachine-based target isolation and signal transduction protocols developed in this project offer numerous potential applications in biomedical diagnostics, environmental monitoring, and forensic analysis.

Enhanced sensitivity detection of protein immobilization by fluorescent interference on oxidized silicon.

We present a silicon chip-based approach for the enhanced sensitivity detection of surface-immobilized fluorescent molecules. Green fluorescent protein (GFP) is bound to the silicon substrate by a disuccinimidyl terephtalate-aminosilane immobilization procedure. The immobilized organic layers are characterized by surface analysis techniques, like ellipsometry, atomic force microscopy (AFM) and X-ray induced photoelectron spectroscopy. We obtain a 20-fold enhancement of the fluorescent signal, using constructive interference effects in a fused silica dielectric layer, deposited before immobilization onto the silicon. Our method opens perspectives to increase by an order of magnitude the fluorescent response of surface immobilized DNA- or protein-based layers for a variety of biosensor applications.