HARP: A Dynamic Inertial Spectral Partitioner

Partitioning unstructured graphs is central to the parallel solution of computational science and engineering problems. Spectral partitioners, such recursive spectral bisection (RSB), have proven effecfive in generating high-quality partitions of realistically-sized meshes. The major problem which hindered their wide-spread use was their long execution times. This paper presents a new inertial spectral partitioner, called HARP. The main objective of the proposed approach is to quickly partition the meshes at runtime in a manner that works efficiently for real applications in the context of distributed-memory machines. The underlying principle of HARP is to find the eigenvectors of the unpartitioned vertices and then project them onto the eigerivectors of the original mesh. Results for various meshes ranging in size from 1000 to 100,000 vertices indicate that HARP can indeed partition meshes rapidly at runtime. Experimental results show that our largest mesh can be partitioned sequentially in only a few seconds on an SP2 which is several times faster than other spectral partitioners while maintaining the solution quality of the proven RSB method. A parallel WI version of HARP has also been implemented on IBM SP2 and Cray T3E. Parallel HARP, running on 64 processors SP2 and T3E, can partition a mesh containing more than 100,000 vertices into 64 subgrids in about half a second. These results indicate that graph partitioning can now be truly embedded in dynamically-changing real-world applications

In-between spaces of policy and practice: Voices from Prince Edward Island early childhood educators

Over the course of the past decades, the discourse, pedagogy, scope, and delivery of early learning and child care (ELCC) has undergone myriad significant changes internationally, nationally, and at local levels. Prince Edward Island (PEI), the smallest Canadian Province, has not been exempt from these transformations. By situating early childhood educators (ECEs) at the centre of ecological multilevel environments (Bronfenbrenner, 2005), this qualitative study explored how a system-wide change implemented through the Prince Edward Island Preschool Excellence Initiative (PEIPEI) has impacted and is being impacted by ECEs over time. Purposive sampling was used to invite seven early childhood educators working on provincially regulated early years centres (EYCs) to participate in individual interviews. Findings indicated that ECEs have been striving to navigate and merge the space in-between policy and practices and that after ten years, they remain in this liminal space where they continue to navigate unravelling transitions as they search for their professional identity

Plasmid analysis, comparative genomics and transcriptomics of beer-spoilage lactic acid bacteria emphasizing the role of dissolved carbon dioxide and traditional beer-spoilage markers

Specific isolates of lactic acid bacteria (LAB) are capable of growing in and spoiling beer, and are the cause of product and process contamination, and financial loss for brewers the world over. To date, our understanding of how these contaminants are able to grow in beer is limited to analysis of hop-tolerance mechanisms, with a limited number of putative hop-tolerance genes having been described. In order to demonstrate that these hop-tolerance genes are incomplete descriptors of overall beer-spoilage ability, the transcriptional activity of these genes in two different beer-spoilage related (BSR) LAB isolates, and the prevalence and sequence conservation of hop-tolerance gene horC in BSR LAB with varying beer-spoilage ability is examined. This analysis is followed by work demonstrating that the total plasmid profile of a beer-spoilage LAB, and not just plasmids harboring hop-tolerance genes, contributes to the isolate’s overall beer-spoilage phenotype and highlights redundancy in potential beer-spoilage mechanisms. The next chapter provides evidence that the presence of dissolved CO2 (dCO2) in beer selects for the ability of LAB to spoil packaged beer, and that tolerance to this stress is not correlated with hop-tolerance, indicating that dCO2 stress is an important part of the total beer environment. This is followed by the presentation and analysis of the genome of the rapid beer-spoiling isolate Lactobacillus brevis BSO 464 and subsequent RNA sequencing for this isolate when grown in degassed and gassed beer so as to elucidate which genes are active when grown in beer, and when grown specifically in the presence of dCO2. Global transcriptome sequencing of this L. brevis isolate and Pediococcus claussenii ATCC BAA-344T when each were grown in growth-limiting concentrations of hops was also performed in order to clarify the hop-specific transcriptional response from that of the response when these isolates grow in the total beer environment. Lastly, comparison is made between available genomes of BSR LAB to reveal that the specific brewery environment a BSR LAB is recovered from, influences genetic variability and that comparison within a given LAB species reveals genetic differences that can be exploited as beer-spoilage genetic markers. This comparative analysis reveals that the total plasmid-coding capacity strongly influences individual BSR LAB beer-spoilage phenotype and the environment they are able to grow in. Overall, beer-spoilage ability is shown to be adaptive and acquired incrementally and not solely as a result of the presence of hop-tolerance genes

An Information-Theoretic Approach to Optimize JWST Observations and Retrievals of Transiting Exoplanet Atmospheres

We provide an example of an analysis to explore the optimization of observations of transiting hot jupiters with JWST to characterize their atmospheres, based on a simple three-parameter forward model. We construct expansive forward model sets for eleven hot jupiters, ten of which are relatively well-characterized, exploring a range of parameters such as equilibrium temperature and metallicity, as well as considering host stars over a wide range in brightness. We compute posterior distributions of our model parameters for each planet with all of the available JWST spectroscopic modes and several programs of combined observations and compute their effectiveness using the metric of estimated mutual information per degree of freedom. From these simulations, clear trends emerge that provide guidelines for designing a JWST observing program. We demonstrate that these guidelines apply over a wide range of planet parameters and target brightnesses for our simple forward model.Comment: Accepted to ApJ, 25 pages, 14 figures, 8 table

A strategy for mapping unstructured mesh computational mechanics programs onto distributed memory parallel architectures

The motivation of this thesis was to develop strategies that would enable unstructured mesh based computational mechanics codes to exploit the computational advantages offered by distributed memory parallel processors. Strategies that successfully map structured mesh codes onto parallel machines have been developed over the previous decade and used to build a toolkit for automation of the parallelisation process. Extension of the capabilities of this toolkit to include unstructured mesh codes requires new strategies to be developed. This thesis examines the method of parallelisation by geometric domain decomposition using the single program multi data programming paradigm with explicit message passing. This technique involves splitting (decomposing) the problem definition into P parts that may be distributed over P processors in a parallel machine. Each processor runs the same program and operates only on its part of the problem. Messages passed between the processors allow data exchange to maintain consistency with the original algorithm. The strategies developed to parallelise unstructured mesh codes should meet a number of requirements: The algorithms are faithfully reproduced in parallel. The code is largely unaltered in the parallel version. The parallel efficiency is maximised. The techniques should scale to highly parallel systems. The parallelisation process should become automated. Techniques and strategies that meet these requirements are developed and tested in this dissertation using a state of the art integrated computational fluid dynamics and solid mechanics code. The results presented demonstrate the importance of the problem partition in the definition of inter-processor communication and hence parallel performance. The classical measure of partition quality based on the number of cut edges in the mesh partition can be inadequate for real parallel machines. Consideration of the topology of the parallel machine in the mesh partition is demonstrated to be a more significant factor than the number of cut edges in the achieved parallel efficiency. It is shown to be advantageous to allow an increase in the volume of communication in order to achieve an efficient mapping dominated by localised communications. The limitation to parallel performance resulting from communication startup latency is clearly revealed together with strategies to minimise the effect. The generic application of the techniques to other unstructured mesh codes is discussed in the context of automation of the parallelisation process. Automation of parallelisation based on the developed strategies is presented as possible through the use of run time inspector loops to accurately determine the dependencies that define the necessary inter-processor communication

Towards establishing a fit-for-purpose regulatory framework for radiation protection in Western Australia\u27s mining industry: Evaluating mine worker exposures to naturally occurring radionuclides

Mining in the state of Western Australia (WA) formally commenced in the 1840s, and over the ensuing 180 years has evolved to be the epicentre of the Australian mining industry and a significant contributor to the national economy. The lithology of WA is replete with mineralisation that hosts uranium and “critical minerals” required for the global renewable energy sector. The state’s first uranium mine is under development, and high levels of activity are occurring in the state’s nascent critical minerals sector, with 168 WA-based companies pursuing rare earths-bearing minerals, 51 of which are actively drilling on their tenements. WA’s mineral deposits typically contain levels of the naturally occurring radionuclides (NORs) thorium-232 and uranium-238 that are elevated above the global crustal average. Workers are exposed to NORs during the mining and mineral extraction processes, and radiation doses that exceed applicable exposure standards may eventuate. The central issue addressed by this research is “what is the potential for radiation exposures from NORs to the significantly increased workforce, and is the regulatory framework fit-for-purpose to ensure radiation doses are kept as low as reasonably achievable?” The research traces the history of worker radiation doses from 1977 to 2020, finding the maximum dose was 163.4mSv, more than eight times the current derived annual dose limit. Whilst 93.5% of all workers received doses of less than 5.0mSv per year, the potential for elevated doses is ever-present as witnessed by 10.3mSv reported in 2009-10. The increase in activity coincides with a revision of the dose coefficients (DCs) associated with the intake of radionuclides. The research evaluates the revised DCs and forecasts doses from inhalation of radioactive dusts will nearly double, and lead to workers receiving doses exceeding 5mSv for the first time since 2009-10. The research raises issues with the evaluation of worker doses and recommends personal dust sampling be prioritised. The revised DCs reinforce the need for effective long-term management of NOR-contaminated wastes arising from mineral processing activities. The research investigated a technique for the removal and capture of NOR-contaminated scale from a piece of disused mining equipment, reporting capture efficiencies of greater than 90%. The technique has the potential to significantly reduce the environmental footprint of NOR-contaminated wastes and to minimise doses to workers involved in the removal process. The research finds that the current regulatory framework is fit-for-purpose. However, inter-agency relationships require strengthening, and the capacity of the regulator to effectively regulate the current and future number of mining operations is questioned. The mining industry is similarly vulnerable to capability and capacity constraints – but has failed to respond to issues in relation to competent radiation safety officers first raised by the Winn Inquiry in 1984. Disconcertingly, monitoring of worker exposures to NORs reached a nadir in the final years covered by this Thesis, raising questions as to the veracity of worker doses reported to the regulatory agency. Academic papers for publication have been developed and are drawn upon in each Chapter. Six papers have been published in peer-reviewed journals, and a seventh is undergoing the editorial process