Accelerating High-Throughput Computing through OpenCL

This paper presents the implementation of a HTCondor pool with GPU execution capabilities through OpenCL. Implementation is discussed from both the system setup and the software design standpoint. The GPU landscape is investigated and the efficiency of the system is evaluated via Fast- Fourier Transform computations. Experimental results show that HTCondor GPU performance matches a dedicated GPU cluster

Using Machine Learning to Quantify Transverse Plane Lumbopelvic Rhythm

Lumbopelvic rhythm illustrates the relative motion between the lumbar spine and pelvis during various activities and could be used as a biomarker for low back pain (LBP). Sagittal plane lumbopelvic rhythm has been extensively examined as a surrogate to measure low back pain risk factor, but trunk rotation, the second component of lifting is commonly missed. Since lumbopelvic rhythm are time series and not discrete variables, machine learning may be a viable solution in identifying clusters of patterns for healthy adults. PURPOSE: To categorize healthy lumbopelvic rhythm in the transverse plane using machine learning. METHODS: 80 adults with no history of LBP (Young: n = 46; 26.9 ± 6.9 yr; Middle-Age: n = 33; 52.4 ± 6.9 yr). 3D kinematics of the lumbar spine and pelvis were calculated as participants performed maximal trunk rotation from right to left. Coupling angles were calculated using vector coding and represented in 4 coordination patterns (in-phase, anti-phase, superior-only, inferior-only). K-means clustering (k = 3) was used to segment coupling angles into clusters. Within each cluster, the age groups were compared. RESULTS: 3 distinct movement patterns were discovered (Figure 1). Lumbar spine and pelvis mostly moved in-phase, but for cluster 1, the start and end of the lumbar and pelvis was in anti-phase, while cluster 2 and 3 started and ended in-phase. Cluster 2 switched from in- to anti- and back to in-phase in the start and during transitioning directions. Age differences were seen only in cluster 1 where young and middle-age adults started rotation in anti-phase, but middle-age adults ended the rotation by only moving the lumbar spine and young adults ended in anti-phase. CONCLUSION: These movement patterns represent the different ways a healthy individual may perform trunk rotation, which along with sagittal plane motion can potentially be used to identify individuals with LBP.https://digitalcommons.odu.edu/gradposters2021_healthsciences/1007/thumbnail.jp

iCurate: A Research Data Management System

Scientific research activities generate a large amount of data, which varies in format, volume, structure and ownership. Although there are revision control systems and databases developed for data archiving, the traditional data management methods are not suitable for High Performance Computing (HPC) systems. The files in such systems do not have semantic annotations and cannot be archived and managed for public dissemination. We have proposed and developed a Research Data Management (RDM)system, iCurate', which provides easy-to-use RDM facilities with semantic annotations. The system incorporates Metadata Retrieval, Departmental Archiving, Workflow Management System, Meta data Validation and Self Inferencing. The `i' emphasises the user-oriented design. iCurate will support researchers by annotating their data in a clearer and machine readable way from its production to publication for the future reus

Disorder and Doping in the Oxygenated Electron-doped Superconductor PCCO

This thesis is composed of two parts: the first part deals with the high temperature electron-doped superconductor Pr_(2-x)Ce_(x)CuO_(4-delta); the second part deals with the diluted magnetic semiconductor Ti_(1-x)Co_(x)O_(2-delta). It is not clear why oxygen reduction and cerium doping are necessary to obtain superconductivity in the electron-doped Pr_(2-x)Ce_(x)CuO_(4-delta). I investigated the effects of oxygenation in this material using resistivity and Hall measurements. For various oxygen contents, I was able to determine that there is a separable doping and a disorder contribution to the superconducting transition temperature. I was able to quantitatively separate out these two effects and show that these two effects are opposite with regards to changes in T_(c) for overdoped thin films. The disorder component is roughly twice as large as the doping component. This analysis is also shown to be self consistent in demonstrating that the doping component of oxygen variation follows the trends of Cerium doping. For the diluted magnetic semiconductor Ti_(1-x)Co_(x)O_(2-delta), I investigated the intrinsic nature of the ferromagnetism observed in thin films. Hall effect measurements were used as the technique because ferromagnetic materials exhibit an anomalous Hall effect, which is due to an interaction between the charge carriers and the magnetic moments. I found that low carrier concentration anatase phase films did not exhibit an anomalous Hall effect, whereas high carrier concentration rutile phase films do. The presence of the anomalous Hall effect at this point cannot be attributed to an intrinsic ferromagnetism as cobalt clusters are observed in these films

Towards Modern, Accessible and Dynamic HPC Using Container-based Virtual Clusters

In this thesis, a novel Virtual Container Cluster (VCC) framework is presented. Despite the growing popularity of container virtualisation in order to increase the flexi-bility of the software stack, run time environment virtualisation still poses significant portability challenges; by depending on the underlying cluster execution paradigm,a niche class of HPC only containers has emerged. This trend is detrimental to reusability, reproducibility, and encouraging new communities to HPC. Traditional virtualisation techniques have a rich history within HPC, and have been demonstrated to offer much more than software flexibility. A Virtual Machine by nature requires an OS and full stack environment akin to a physical machine, and this allows it to be instantiated regardless of the underlying machine and what services it provides. This capability is essential in order to implement job forwarding and spanning - where the burden of an entire job can be transferred or shared between hetero-geneous cluster systems - with a high level of confidence that the environments will be compatible. In turn, this brings improvements to global resource performance, reducing the job turnaround time and increasing cluster utilization. The VCC is an innovative solution that combines the full stack and container virtualisation approaches. Therefore, it offers both the flexibility of containers with the improved portability, performance and scalability of the full stack approach. In order to maintain the same accessibility and lower barrier of entry as the run time environment approach, the design incorporates an autonomous configuration and contextualisation mechanism, along with a Software Defined Networking technology, to ensure the full stack container does not place an additional burden on the user. The usefulness and performance is validated through benchmarking and two case studies: virtual clusters in the classroom and inter-institutional spanning

VCC: A framework for building containerized reproducible cluster software environments

The problem of portability and reproducibility of the software used to conduct computational experiments has recently come to the fore. Container virtualisation has proved to be a powerful tool to achieve portability of a code and it's execution environment, through runtimes such as Docker, LXC, Singularity and others - without the performance cost of traditional Virtual Machines (Chamberlain, Invenshure, and Schommer 2014; Felter et al. 2014). However, scientific software often depends on a system foundation that provides middleware, libraries, and other supporting software in order for the code to execute as intended. Typically, container virtualisation addresses only the portability of the code itself, which does not make it inherently reproducible. For example, a containerized MPI application may offer binary compatibility between different systems, but for execution as intended, it must be run on an existing cluster that provides the correct interfaces for parallel MPI execution. As a greater demand to accomodate a diverse range of disciplines is placed on high performance and cluster resources, the ability to quickly create and teardown reproducible, transitory virtual environments that are tailored for an individual task or experiment will be essential. The Virtual Container Cluster (VCC) is a framework for building containers that achieve this goal, by encapsulating a parallel application along with an execution model, through a set of dependency linked services and built-in process orchestration. This promotes a high degree of portability, and offers easier reproducibility by shipping the application along with the foundation required to execute it - whether that be an MPI cluster, big data processing framework, bioinformatics pipeline, or any other execution model (Higgins, Holmes, and Venters 2017)

Design and Testing of a Scale-Model Surface Undersea Kite

Surface Undersea Kites (SUSK) is a concept for extracting energy from tidal flows. Existing work in Airborne Wind Energy and Tethered Undersea Kites has shown tethered kites to be a viable renewable energy technology in air and water currents. SUSK employs a tethered boat with a submerged, vertical wing rather than a fully submerged kite to eliminate underwater tether drag. A scale-model SUSK system has been designed and constructed using mainly 3D printed components. Dynamic simulations of the system have also been developed to obtain power estimates for the scale-model and full-size SUSK systems. The scale-model system was tested in a large water flume, and its performance was comparable to that predicted by the dynamic simulations. Recommendations are made to improve the SUSK design