Effects of Communication Protocol Stack Offload on Parallel Performance in Clusters

The primary research objective of this dissertation is to demonstrate that the effects of communication protocol stack offload (CPSO) on application execution time can be attributed to the following two complementary sources. First, the application-specific computation may be executed concurrently with the asynchronous communication performed by the communication protocol stack offload engine. Second, the protocol stack processing can be accelerated or decelerated by the offload engine. These two types of performance effects can be quantified with the use of the degree of overlapping Do and degree of acceleration Daccs. The composite communication speedup metrics S_comm(Do, Daccs) can be used in order to quantify the combined effects of the protocol stack offload. This dissertation thesis is validated empirically. The degree of overlapping Do, the degree of acceleration Daccs, and the communication speedup Scomm characteristic of the system configurations under test are derived in the course of experiments performed for the system configurations of interest. It is shown that the proposed metrics adequately describe the effects of the protocol stack offload on the application execution time. Additionally, a set of analytical models of the networking subsystem of a PC-based cluster node is developed. As a result of the modeling, the metrics Do, Daccs, and Scomm are obtained. The models are evaluated as to their complexity and precision by comparing the modeling results with the measured values of Do, Daccs, and Scomm. The primary contributions of this dissertation research are as follows. First, the metric Daccs and Scomm are introduced in order to complement the Do metric in its use for evaluation of the effects of optimizations in the networking subsystem on parallel performance in clusters. The metrics are shown to adequately describe CPSO performance effects. Second, a method for assessing performance effects of CPSO scenarios on application performance is developed and presented. Third, a set of analytical models of cluster node networking subsystems with CPSO capability is developed and characterised as to their complexity and precision of the prediction of the Do and Daccs metrics

Modelling polymer electrolyte membrane fuel cells for dynamic reliability assessment

Tackling climate change is arguably the biggest challenge humanity faces in the 21st century. Rising average global temperatures threaten to destabilize the fragile ecosystem of the Earth and bring unprecedented changes to human lives if nothing is done to prevent it. This phenomenon is caused by the anthropogenic greenhouse effect due to the increasing atmospheric concentrations of carbon dioxide (CO2). One way to avert the disaster is to drastically reduce the consumption of fossil fuels in all spheres of human activities, including transportation. To do this, research and development of electric vehicles (EVs) to make them more efficient, reliable and accessible is essential. [Continues.

SYSTEMATIC INVESTIGATION OF QUORUM SENSING IN Escherichia coli

High throughput techniques and advanced mathematical tools have enabled systematic investigations of biological systems with unparalleled precision. Not only molecular interactions between components but mechanisms and the dynamic behaviors associated with these systems are revealed, suggesting that comprehensive systems biology can be realized in the near future. Quorum sensing, especially the auto-inducer2 (AI-2) system, has been extensively studied due to its commonality among bacteria and connections to pathogenic phenotypes. In this study, the E. coli quorum sensing AI-2 system was studied combing system-based mathematical modeling and high throughput genomic profiling. First, a Stochastic Petri Network (SPN) model was constructed based on available regulatory information. Simulations together with experimental data demonstrated that the apparent stimulation of AI-2 in the presence of glucose is not from the increased transcriptional or translational expression of AI-2 synthases luxS and pfs, nor from the increased metabolic flux associated with LuxS-related pathways but from an alternative AI-2 synthesis pathway. The conversion of adenosine with cellular extracts from both luxS and pfs mutants validated our prediction about the existence of an alternative non-LuxS related AI-2 synthesis pathway. Second, AI-2 uptake regulatory network was investigated in detail: lsrR-lacZ, lsrK-lacZ fusion reporters were constructed and the analysis found that lsrR is subject to its own repression and is induced by both lsrK and luxS. Further transcriptome analysis demonstrated that lsrR and lsrK, together with quorum signal AI-2, coregulate lsrRK regulon, which influences phenotypes (biofilm, small RNAs). Importantly, this regulation is in a distinctly different manner than that mediating the lsr operon. We hypothesize that lsrR acts together with AI-2 to mediate cellular processes and that the phosphorylation of AI-2 molecule through lsrK triggers different response pathways. These investigations demonstrated that lsrR, lsrK are indispensable for AI-2 uptake. These newly elucidated regulatory mechanisms and associations undoubtedly broaden the scope of the AI-2 quorum sensing system, and provide a solid foundation for further mathematical modeling of the dynamics and system behaviors in E. coli . Finally, a tight coupling of experimental manipulation with mathematical analysis, as demonstrated in this study, provides a good example for systematically investigating biological systems

Parallel simulation techniques for telecommunication network modelling

In this thesis, we consider the application of parallel simulation to the performance modelling of telecommunication networks. A largely automated approach was first explored using a parallelizing compiler to speed up the simulation of simple models of circuit-switched networks. This yielded reasonable results for relatively little effort compared with other approaches. However, more complex simulation models of packet- and cell-based telecommunication networks, requiring the use of discrete event techniques, need an alternative approach. A critical review of parallel discrete event simulation indicated that a distributed model components approach using conservative or optimistic synchronization would be worth exploring. Experiments were therefore conducted using simulation models of queuing networks and Asynchronous Transfer Mode (ATM) networks to explore the potential speed-up possible using this approach. Specifically, it is shown that these techniques can be used successfully to speed-up the execution of useful telecommunication network simulations. A detailed investigation has demonstrated that conservative synchronization performs very well for applications with good look ahead properties and sufficient message traffic density and, given such properties, will significantly outperform optimistic synchronization. Optimistic synchronization, however, gives reasonable speed-up for models with a wider range of such properties and can be optimized for speed-up and memory usage at run time. Thus, it is confirmed as being more generally applicable particularly as model development is somewhat easier than for conservative synchronization. This has to be balanced against the more difficult task of developing and debugging an optimistic synchronization kernel and the application models

The doctoral research abstracts. Vol:7 2015 / Institute of Graduate Studies, UiTM

Foreword: The Seventh Issue of The Doctoral Research Abstracts captures the novelty of 65 doctorates receiving their scrolls in UiTM’s 82nd Convocation in the field of Science and Technology, Business and Administration, and Social Science and Humanities. To the recipients I would like to say that you have most certainly done UiTM proud by journeying through the scholastic path with its endless challenges and impediments, and persevering right till the very end. This convocation should not be regarded as the end of your highest scholarly achievement and contribution to the body of knowledge but rather as the beginning of embarking into high impact innovative research for the community and country from knowledge gained during this academic journey. As alumni of UiTM, we will always hold you dear to our hearts. A new ‘handshake’ is about to take place between you and UiTM as joint collaborators in future research undertakings. I envisioned a strong research pact between you as our alumni and UiTM in breaking the frontier of knowledge through research. I wish you all the best in your endeavour and may I offer my congratulations to all the graduands. ‘UiTM sentiasa dihati ku’ / Tan Sri Dato’ Sri Prof Ir Dr Sahol Hamid Abu Bakar , FASc, PEng Vice Chancellor Universiti Teknologi MAR

Simulation and design of storage area network

Master'sMASTER OF ENGINEERIN

Assuring virtual network reliability and resilience

A framework developed that uses reliability block diagrams and continuous-time Markov chains to model and analyse the reliability and availability of a Virtual Network Environment (VNE). In addition, to minimize the unpredicted failures and reduce the impact of failure on a virtual network, a dynamic solution proposed for detecting a failure before it occurs in the VNE. Moreover, to predict failure and establish a tolerable maintenance plan before failure occurs in the VNE, a failure prediction method for VNE can be used to minimise the unpredicted failures, reduce backup redundancy and maximise system performance

From Microbial Communities to Distributed Computing Systems

A distributed biological system can be defined as a system whose components are located in different subpopulations, which communicate and coordinate their actions through interpopulation messages and interactions. We see that distributed systems are pervasive in nature, performing computation across all scales, from microbial communities to a flock of birds. We often observe that information processing within communities exhibits a complexity far greater than any single organism. Synthetic biology is an area of research which aims to design and build synthetic biological machines from biological parts to perform a defined function, in a manner similar to the engineering disciplines. However, the field has reached a bottleneck in the complexity of the genetic networks that we can implement using monocultures, facing constraints from metabolic burden and genetic interference. This makes building distributed biological systems an attractive prospect for synthetic biology that would alleviate these constraints and allow us to expand the applications of our systems into areas including complex biosensing and diagnostic tools, bioprocess control and the monitoring of industrial processes. In this review we will discuss the fundamental limitations we face when engineering functionality with a monoculture, and the key areas where distributed systems can provide an advantage. We cite evidence from natural systems that support arguments in favor of distributed systems to overcome the limitations of monocultures. Following this we conduct a comprehensive overview of the synthetic communities that have been built to date, and the components that have been used. The potential computational capabilities of communities are discussed, along with some of the applications that these will be useful for. We discuss some of the challenges with building co-cultures, including the problem of competitive exclusion and maintenance of desired community composition. Finally, we assess computational frameworks currently available to aide in the design of microbial communities and identify areas where we lack the necessary tool

Reversible Computation: Extending Horizons of Computing

This open access State-of-the-Art Survey presents the main recent scientific outcomes in the area of reversible computation, focusing on those that have emerged during COST Action IC1405 "Reversible Computation - Extending Horizons of Computing", a European research network that operated from May 2015 to April 2019. Reversible computation is a new paradigm that extends the traditional forwards-only mode of computation with the ability to execute in reverse, so that computation can run backwards as easily and naturally as forwards. It aims to deliver novel computing devices and software, and to enhance existing systems by equipping them with reversibility. There are many potential applications of reversible computation, including languages and software tools for reliable and recovery-oriented distributed systems and revolutionary reversible logic gates and circuits, but they can only be realized and have lasting effect if conceptual and firm theoretical foundations are established first