La croissance exponentielle de la génération de données pour la bioinformatique couplée à une stagnation des fréquences d’horloge des processeurs modernes accentuent la nécessité de fournir des implémentation tirant bénéfice des capacités parallèles des ordinateurs modernes. Cette thèse se concentre sur des algorithmes et implementations pour des problèmes de bioinformatique. Plusieurs types de parallélisme sont décrits et exploités. Cette thèse présente des applications en génétique, avec un outil de détection de QTL paralllisé sur GPU, en comparaison de structures de protéines, avec un outil permettant de trouver des régions similaires entre protéines parallélisé sur CPU, ainsi qu’à l’analyse de larges graphes avec une implémentation multi-GPUs d’un nouvel algorithme pour le problème du «All-Pairs Shortest Path». / The exponential growth in bioinformatics data generation and the stagnation of processor frequencies in modern processors stress the need for efficient implementations that fully exploit the parallel capabilities offered by modern computers. This thesis focuses on parallel algorithms and implementations for bioinformatics problems. Various types of parallelism are described and exploited. This thesis presents applications in genetics with a GPU parallel tool for QTL detection, in protein structure comparison with a multicore parallel tool for finding similar regions between proteins, and large graph analysis with a multi-GPU parallel implementation for a novel algorithm for the All-Pairs Shortest Path problem.

Over the last few years, flexible electronic systems have gained increased attention from researchers around the world because of their potential to create new applications such as flexible displays, flexible energy harvesters, artificial skin, and health monitoring systems that cannot be integrated with conventional wafer based complementary metal oxide semiconductor processes. Most of the current efforts to create flexible high performance devices are based on the use of organic semiconductors. However, inherent material's limitations make them unsuitable for big data processing and high speed communications. The objective of my doctoral dissertation is to develop integration processes that allow the transformation of rigid high performance electronics into flexible ones while maintaining their performance and cost. In this work, two different techniques to transform inorganic complementary metal-oxide-semiconductor electronics into flexible ones have been developed using industry compatible processes. Furthermore, these techniques were used to realize flexible discrete devices and circuits which include metal-oxide-semiconductor field-effect-transistors, the first demonstration of flexible Fin-field-effect-transistors, and metal-oxide-semiconductors-based circuits. Finally, this thesis presents a new technique to package, integrate, and interconnect flexible high performance electronics using low cost additive manufacturing techniques such as 3D printing and inkjet printing. This thesis contains in depth studies on electrical, mechanical, and thermal properties of the fabricated devices.

It was observed, that the RT-PICLS code ran by FWKT on the hypnos cluster was producing an unusual amount of system load, according to Ganglia metrics. Since this may point to an IO-problem in the code, this code was analyzed more closely.

The importance of stencil-based algorithms in computational science has focused attention on optimized parallel implementations for multilevel cache-based processors. Temporal blocking schemes leverage the large bandwidth and low latency of caches to accelerate stencil updates and approach theoretical peak performance. A key ingredient is the reduction of data traffic across slow data paths, especially the main memory interface. Most of the established work concentrates on updating separate cache blocks per thread, which works on all types of shared memory systems, regardless of whether there is a shared cache among the cores. This approach is memory-bandwidth limited in several situations, where the cache space for each thread can be too small to provide sufficient in-cache data reuse. We introduce a generalized multi-dimensional intra-tile parallelization scheme for shared-cache multicore processors that results in a significant reduction of cache size requirements and shows a large saving in memory bandwidth usage compared to existing approaches. It also provides data access patterns that allow efficient hardware prefetching. Our parameterized thread groups concept provides a controllable trade-off between concurrency and memory usage, shifting the pressure between the memory interface and the Central Processing Unit (CPU).We also introduce efficient diamond tiling structure for both shared memory cache blocking and distributed memory relaxed-synchronization communication, demonstrated using one-dimensional domain decomposition. We describe the approach and our open-source testbed implementation details (called Girih), present performance results on contemporary Intel processors, and apply advanced performance modeling techniques to reconcile the observed performance with hardware capabilities. Furthermore, we conduct a comparison with the state-of-the-art stencil frameworks PLUTO and Pochoir in shared memory, using corner-case stencil operators. We study the impact of the diamond tile size on computational intensity, cache block size, and energy consumption. The impact of computational intensity on power dissipation on the CPU and in the DRAM is investigated and shows that DRAM power is a decisive factor for energy consumption in the Intel Ivy Bridge processor, which is strongly influenced by the computational intensity. Moreover, we show that highest performance does not necessarily lead to lowest energy even if the clock speed is fixed. We apply our approach to an electromagnetic simulation application for solar cell development, demonstrating several-fold speedup compared to an efficient spatially blocked variant. Finally, we discuss the integration of our approach with other techniques for future High Performance Computing (HPC) systems, which are expected to be more memory bandwidth-starved with a deeper memory hierarchy.

The size and complexity of many scientific and enterprise-level applications require a high degree of parallelization in order to produce outputs within an acceptable period of time. This often necessitates the uses of high performance computing clusters (HPCCs) and parallelized applications which are carefully designed and optimized. A myriad of papers study the various factors which influence performance and then attempt to quantify the maximum theoretical speedup that can be achieved by a cluster relative to a sequential processor. The studies tend to only investigate the influences in isolation, but in practice these factors tend to be interdependent. It is the interaction rather than any solitary influence which normally creates the bounds of the design trade space. In the attempt to address this disconnect, this thesis blends the studies into an expanded speedup model which captures the interplay. The model is intended to help the cluster engineer make initial estimates during the early phases of design while the system is not mature enough for refinement using timing studies. The model pulls together factors such as problem scaling, resource allocation, critical sections, and the problem's inherent parallelizability. The derivation was examined theoretically and then validated by timing studies on a physical HPCC. The validation studies found that the model was an adequate generic first approximation. However, it was also found that customizations may be needed in order to account for application-specific influences such as bandwidth limitations and communication delays which are not readily incorporated into a generic model. / Master of Science

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In the thesis we have defined what is understood as a high health organization, and this in comparison with what is commonly known as a high performance organization. While much research is undertaken around high performance organizations, little or no research is undertaken around high health organizations. The thesis attempts to find answers to what it takes to be or to become a high health organization, and how organizations could create such a place, or possibly better “space”. Indeed, a high health organization is not a place, a building, or on organizational structure; it is a state of mind, a purpose, a form of coherence. The work in this thesis is by definition multidisciplinary and systemic, rooted in three, for the purpose, complementary research areas. Workplace spirituality is slowly making its recognition in the management literature, though still too much as a discipline in itself. Ayurveda, the thousands of years old wisdom tradition around systemic health, living systems and purposefulness does get some attention in academic work, however mainly within its cultural roots (of India). Finally, systemic thinking, not really mainstream yet either, is a scientific discipline that did find its way in the sciences, but is much less popular and use in management studies. As argued, we think that in the intersection of workplace spirituality, Ayurveda and systemics, a real new concept of a high health organization is emerging. Key concepts identified in the introduction were consciousness and coherence, which they play an important role in the entire thesis. The prevailing management research is based on an ontology of materialism, while it is clear that workplace spirituality, Ayurveda and systemics do not necessarily fit such an ontology. We have commented on an ontology of non-materialism, based on complexity theory and in particular the understanding of complex adaptive systems. If we would like to explore the concept of a high health organization, an adequate ontology (and epistemology) is necessary. It is impossible to develop a non-materialistic concepts within a materialistic ontology. The consequence of this ontological choice for our research methods are multiple and innovative. Our research method goes beyond deterministic causality, and attempts to visualize entanglement. It can only be based on a much more systemic analysis than what we are used to, hence we use Artificial Neural Networks and Semantics as analytical tools. Based on the results of our field research, the high health organization in a nutshell has the following components: 1. A systemic, values-based vision is the lighthouse of the high health organization 2. Values, and in particular lived values, are the driver of the high health organization 3. Transparent, clear, respectful and non-violent communication is the binding factor 4. A knowledge and learning culture is the necessary condition for a healthy organization 5. Organisational consciousness in the organization is the sufficient condition

The main objective of this study was to measure the nutritional status of iron and vitamin D in varsity female athletes from the University of Ottawa and the possible relationship with their dietary patterns (mixed diet or plant-based diet). Among 63 athletes interested in participating, 17 completed the study. Nutritional intakes were assessed during sports season using two 24-hour recalls with the self-administered dietary assessment tool (ASA24). A blood sample was taken to measure indicators of iron and vitamin D status. The results revealed that 5% of the athletes suffered from vitamin D deficiency and as much as 47% had suboptimal vitamin D levels. No athletes suffered from iron deficiency anemia (IDA), but 26% had iron deficiency (ID). The vitamin D intake for 94% of athletes was below the estimated average requirements (EAR) and the use of supplements helped athletes attain the EAR. In contrast, 94% of athletes were able to meet the EAR for iron and the use of supplements caused athletes to exceed upper limits (UL). Lastly, due to the small number of plant-based athletes recruited, it was not possible to establish any relationships with this dietary pattern.

High-performance athletes' (HPAs) engagement in proactive retirement preparation has become increasingly important for their well-being and quality of life during and after sport. As researchers continue to highlight the plethora of challenges underprepared HPAs face when retiring from sport, retirement support available to Canadian HPAs through Game Plan continues to be significantly underutilized (Game Plan, 2023). Researchers have identified environmental barriers as an influencing factor determining athletes' ability to access and utilize available forms of retirement support (Brassard et al., 2022). Current literature lacks the use of a holistic lens to identify the organizational factors that act as barriers and facilitators faced by athletes in this regard. An exploration with this lens could enhance our understanding of HPAs' ability to prepare for retirement by providing insights into the organizational interplay sport members have in facilitating a sport environment that enables, restricts, or hinders a HPA's ability to prepare for life after sport. Furthermore, a holistic lens can provide researchers with the necessary information to develop further frameworks and strategies to minimize athlete retirement barriers (Stambulova et al., 2020). The purpose of this doctoral dissertation is to address this gap through the following objectives: (a) examine how active and retired athletes utilized retirement support mechanisms, (b) explore high-performance sport members' perspectives and understanding of retirement support mechanisms, and (c) facilitate co-design sessions to innovate solution-driven prototypes to address sport members' athlete retirement needs. The methodologies of Bronfenbrenner's Ecological Systems theory and Design Thinking were adopted to guide and facilitate this research. This dissertation is composed of three articles, each correlating with the research objectives. With the first research objective, a secondary data analysis was used to examine how athletes in the Canadian sport system were utilizing Game Plan's resources from 2019-2021. This examination provided insight into athletes' Game Plan usage discrepancies when drawing comparisons to the funding each National Sport Organization (NSO) earned, their league of competition (e.g., Para or Non-Para sport), and repeat uses of Game Plan's resources after an initial interaction. As a result of the findings from this examination, considerations are proposed for sport organizations who seek to improve their athlete engagement with Game Plan's retirement resources. The second objective was investigated through empathy interviews (Kelley & Kelley, 2013) conducted with active athletes, retired athletes, support personnel, and performance partners across the sport system. A total of 19 individuals were interviewed. Empathy interviews were used to create personas for each role. Findings from this exploration add to the literature by outlining the following empirical findings: (a) high-performance sport members have limited knowledge and understanding of accessible retirement resources, (b) sport organizations' cultures can present barriers or facilitators through direct and indirect messages to athletes, and (c) HPAs who proactively sought out support or had a good sport-life balance experienced fewer challenges adapting to life after sport. The third and final objective was supported via the Stanford d. school's five-step Design Thinking model: empathize, define, ideate, prototype, and test. This section of research consisted of a co-design session conducted with two groups of participants. In each session, participants were led through brainstorming cluster activities to define, ideate, design, and evaluate athlete retirement solution-driven prototypes. Sport members collaboratively designed the following three evidenced-based prototypes: (a) creating a new funding metrics system, (b) strengthening collaboration between NSOs and Game Plan, and (c) enhancing athlete retirement coach education. The Design Thinking process as well as the insights outlining why and how the adoption of each prototype can advance HPAs' ability to prepare for their lives after sport are discussed. This article is the first to adopt a Design Thinking approach to advance athlete retirement literature and aims to serve as a catalyst for researchers to adopt Design Thinking methods to further the field of sport performance psychology. The results of this doctoral dissertation research add empirical, theoretical, and methodological contributions to both the athlete retirement and Design Thinking literature.