Doctor of Philosophy

dissertationRecent trends in high performance computing present larger and more diverse computers using multicore nodes possibly with accelerators and/or coprocessors and reduced memory. These changes pose formidable challenges for applications code to attain scalability. Software frameworks that execute machine-independent applications code using a runtime system that shields users from architectural complexities oer a portable solution for easy programming. The Uintah framework, for example, solves a broad class of large-scale problems on structured adaptive grids using fluid-flow solvers coupled with particle-based solids methods. However, the original Uintah code had limited scalability as tasks were run in a predefined order based solely on static analysis of the task graph and used only message passing interface (MPI) for parallelism. By using a new hybrid multithread and MPI runtime system, this research has made it possible for Uintah to scale to 700K central processing unit (CPU) cores when solving challenging fluid-structure interaction problems. Those problems often involve moving objects with adaptive mesh refinement and thus with highly variable and unpredictable work patterns. This research has also demonstrated an ability to run capability jobs on the heterogeneous systems with Nvidia graphics processing unit (GPU) accelerators or Intel Xeon Phi coprocessors. The new runtime system for Uintah executes directed acyclic graphs of computational tasks with a scalable asynchronous and dynamic runtime system for multicore CPUs and/or accelerators/coprocessors on a node. Uintah's clear separation between application and runtime code has led to scalability increases without significant changes to application code. This research concludes that the adaptive directed acyclic graph (DAG)-based approach provides a very powerful abstraction for solving challenging multiscale multiphysics engineering problems. Excellent scalability with regard to the different processors and communications performance are achieved on some of the largest and most powerful computers available today

Uintah hybrid task-based parallelism algorithm

pre-printAbstract-Uintah is a software framework that provides an environment for solving large-scale science and engineering problems involving the solution of partial differential equations. Uintah uses a combination of fluid-flow solvers and particle-based methods for solids, together with adaptive meshing and asynchronous task-based approach with automated load balancing. When applying Uintah to fluid-structure interaction problems, the combination of adaptive meshing and the movement of structures through space present a formidable challenge in terms of achieving scalability on large-scale parallel computers. Adopting a model that uses MPI to communicate between nodes and a shared memory model on-node is one approach to achieve scalability on large-scale systems.This scalability challenge is addressed here for Uintah, by the development of new hybrid runtime and scheduling algorithms combined with novel lock-free data structures, making it possible for Uintah to achieve excellent scalability for a challenging fluid-structure problem with mesh refinement on as many as 256K cores

Investigating applications portability with the Uintah DAG-based runtime system on PetaScale supercomputers

pre-printPresent trends in high performance computing present formidable challenges for applications code using multicore nodes possibly with accelerators and/or co-processors and reduced memory while still attaining scalability. Software frameworks that execute machine-independent applications code using a runtime system that shields users from architectural complexities offer a possible solution. The Uintah framework for example, solves a broad class of large-scale problems on structured adaptive grids using fluid-flow solvers coupled with particle-based solids methods. Uintah executes directed acyclic graphs of computational tasks with a scalable asynchronous and dynamic runtime system for CPU cores and/or accelerators/coprocessors on a node. Uintah's clear separation between application and runtime code has led to scalability increases of 1000x without significant changes to application code. This methodology is tested on three leading Top500 machines; OLCF Titan, TACC Stampede and ALCF Mira using three diverse and challenging applications problems. This investigation of scalability with regard to the different processors and communications performance leads to the overall conclusion that the adaptive DAG-based approach provides a very powerful abstraction for solving challenging multi-scale multi-physics engineering problems on some of the largest and most powerful computers available today

DAG-based software frameworks for PDEs

pre-printThe task-based approach to software and parallelism is well-known and has been proposed as a potential candidate, named the silver model, for exas-cale software. This approach is not yet widely used in the large-scale multi-core parallel computing of complex systems of partial differential equations. After surveying task-based approaches we investigate how well the Uintah software and an extension named Wasatch fit in the task-based paradigm and how well they perform on large scale parallel computers. The conclusion is that these approaches show great promise for petascale but that considerable algorithmic challenges remain

Tao Te Ching : how leaders establish a virtuous circle of non-action and action : a thesis presented in partial fulfilment of the requirements for the degree of Master of Business Studies in Management at Massey University, Albany, New Zealand

This study aims to find a way to establish a virtuous leadership cycle through the exploration of Taoist philosophy. Taoism was created to help ancient Chinese emperors to rule for a long time, and some of its views were also studied and used by some dynasties. Its classic work, Tao Te Ching, includes many discussions about governance, such as action and non-action, and leadership like water. This thesis interprets Taoism from the perspective of modern leadership through the reappearance of its practical history and the textual analysis of Tao Te Ching. Surprisingly, the results show that its content involves at least four modern management fields: leadership, motivation, organizational structure, and strategic planning. It is more like a map to guide leaders on how to use relevant skills

Construction of Clinical Biobanks and the Medical Ethics

Nowadays, various types and forms of clinical biobanks have been gradually established worldwide, which have become one of the important components and research platforms of life science and related disease researches in the medical system. This article mainly introduces the construction, management and operation of clinical biobanks, and discusses the medical ethics faced by it

On the Construction of Biobank in General Hospitals

Objective: Discussion on a series of biospecimen related issues are conducted, such as collection and preservation, quality control, as well as management and application, during the construction of human tissue biobank in a general hospital. Methods: To develop a set of standardized operational procedures and to collect tissue samples, such as whole blood, serum, plasma, fresh frozen tissues, cerebrospinal fluid, and paraffin-embedded tissues, which were classified and made aliquots according to different requirements, and stored at -80℃ temperature refrigerator or in liquid nitrogen. At the same time, a set of information management software was used to realize management of the biobank. Results: Currently, there are more than 20,000 specimens of various benign and malignant cases, which cover 380 diseases, being collected in the biological database in our hospital. These specimens include paraffin-embedded tissue, fresh frozen tissue, femoral head, whole blood, plasma, serum and cerebrospinal fluid, etc. A large number of these specimensare beneficial is used in clinical research at present. Conclusion: The establishment of biological sample bank can maximize the value of non-reborn human tissue specimens, and provide normal control standards as well as benign and malignant disease standards for clinical diagnosis and treatment, which is of great significance to the research of disease pathogenesis and the development of detection technology

An immunization scheme for ransomware

In recent years, as the popularity of anonymous currencies such as Bitcoin has made the tracking of ransomware attackers more difficult, the amount of ransomware attacks against personal computers and enterprise production servers is increasing rapidly. The ransomware has a wide range of influence and spreads all over the world. It is affecting many industries including internet, education, medical care, traditional industry, etc. This paper uses the idea of virus immunity to design an immunization solution for ransomware viruses to solve the problems of traditional ransomware defense methods (such as anti-virus software, firewalls, etc.), which cannot meet the requirements of rapid detection and immediate prevention of new outbreaks attacks. Our scheme includes two parts: server and client. The server provides an immune configuration file and configuration file management functions, including a configuration file module, a cryptography algorithm module, and a display module. The client obtains the immunization configuration file from server in real time, and performs the corresponding operations according to the configuration file to make the computer have an immune function for a specific ransomware, including an update module, a configuration file module, a cryptography algorithm module, a control module, and a log module. This scheme controls mutexes, services, files and registries respectively, to destroy the triggering conditions of the virus and finally achieve the purpose of immunizing a computer from a specific ransomware

Transplantation of human villous trophoblasts preserves cardiac function in mice with acute myocardial infarction

Over the past decade, cell therapies have provided promising strategies for the treatment of ischaemic cardiomyopathy. Particularly, the beneficial effects of stem cells, including bone marrow stem cells (BMSCs), endothelial progenitor cells (EPCs), mesenchymal stem cells (MSCs), embryonic stem cells (ESCs), and induced pluripotent stem cells (iPSCs), have been demonstrated by substantial preclinical and clinical studies. Nevertheless stem cell therapy is not always safe and effective. Hence, there is an urgent need for alternative sources of cells to promote cardiac regeneration. Human villous trophoblasts (HVTs) play key roles in embryonic implantation and placentation. In this study, we show that HVTs can promote tube formation of human umbilical vein endothelial cells (HUVECs) on Matrigel and enhance the resistance of neonatal rat cardiomyocytes (NRCMs) to oxidative stress in vitro. Delivery of HVTs to ischaemic area of heart preserved cardiac function and reduced fibrosis in a mouse model of acute myocardial infarction (AMI). Histological analysis revealed that transplantation of HVTs promoted angiogenesis in AMI mouse hearts. In addition, our data indicate that HVTs exert their therapeutic benefit through paracrine mechanisms. Meanwhile, injection of HVTs to mouse hearts did not elicit severe immune response. Taken together, our study demonstrates HVT may be used as a source for cell therapy or a tool to study cell-derived soluble factors for AMI treatment

Modelling of grinding mechanics : a review

Grinding is one of the most widely used material removal methods at the end of many process chains. Grinding force is related to almost all grinding parameters, which has a great influence on material removal rate, dimensional and shape accuracy, surface and subsurface integrity, thermodynamics, dynamics, wheel durability, and machining system deformation. Considering that grinding force is related to almost all grinding parameters, grinding force can be used to detect grinding wheel wear, energy calculation, chatter suppression, force control and grinding process simulation. Accurate prediction of grinding forces is important for optimizing grinding parameters and the structure of grinding machines and fixtures. Although there are substantial research papers on grinding mechanics, a comprehensive review on the modeling of grinding mechanics is still absent from the literature. To fill this gap, this work reviews and introduces theoretical methods and applications of mechanics in grinding from the aspects of modeling principles, limitations and possible future trendencies