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High availability is a critical feature of data centers, cloud, and cluster computing environments. Replication is a classical approach to increase service availability by providing redundancy. However, traditional replication methods are increasingly unattractive for deployment due to several limitations such as application-level non-transparency, non-isolation of applications (causing security vulnerabilities), complex system management, and high cost. Virtualization overcomes these limitations through another layer of abstraction, and provides high availability through virtual machine (VM) live migration: a guest VM image running on a primary host is transparently check-pointed and migrated, usually at a high frequency, to a backup host, without pausing the VM; the VM is resumed from the latest checkpoint on the backup when a failure occurs. A virtual cluster (VC) generalizes the VM concept for distributed applications and systems: a VC is a set of multiple VMs deployed on different physical machines connected by a virtual network. This dissertation presents a set of VM live migration techniques, their implementations in the Xen hypervisor and Linux operating system kernel, and experimental studies conducted using benchmarks (e.g., SPEC, NPB, Sysbench) and production applications (e.g., Apache webserver, SPECweb). We first present a technique for reducing VM migration downtimes called FGBI. FGBI reduces the dirty memory updates that must be migrated during each migration epoch by tracking memory at block granularity. Additionally, it determines memory blocks with identical content and shares them to reduce the increased memory overheads due to block-level tracking granularity, and uses a hybrid compression mechanism on the dirty blocks to reduce the migration traffic. We implement FGBI in the Xen hypervisor and conduct experimental studies, which reveal that the technique reduces the downtime by 77% and 45% over competitors including LLM and Remus, respectively, with a performance overhead of 13%. We then present a lightweight, globally consistent checkpointing mechanism for virtual cluster, called VPC, which checkpoints the VC for immediate restoration after (one or more) VM failures. VPC predicts the checkpoint-caused page faults during each checkpointing interval, in order to implement a lightweight checkpointing approach for the entire VC. Additionally, it uses a globally consistent checkpointing algorithm, which preserves the global consistency of the VMs' execution and communication states, and only saves the updated memory pages during each checkpointing interval. Our Xen-based implementation and experimental studies reveal that VPC reduces the solo VM downtime by as much as 45% and reduces the entire VC downtime by as much as 50% over competitors including VNsnap, with a memory overhead of 9% and performance overhead of 16%. The dissertation's third contribution is a VM resumption mechanism, called VMresume, which restores a VM from a (potentially large) checkpoint on slow-access storage in a fast and efficient way. VMresume predicts and preloads the memory pages that are most likely to be accessed after the VM's resumption, minimizing otherwise potential performance degradation due to cascading page faults that may occur on VM resumption. Our experimental studies reveal that VM resumption time is reduced by an average of 57% and VM's unusable time is reduced by 73.8% over native Xen's resumption mechanism. Traditional VM live migration mechanisms are based on hypervisors. However, hypervisors are increasingly becoming the source of several major security attacks and flaws. We present a mechanism called HSG-LM that does not involve the hypervisor during live migration. HSG-LM is implemented in the guest OS kernel so that the hypervisor is completely bypassed throughout the entire migration process. The mechanism exploits a hybrid strategy that reaps the benefits of both pre-copy and post-copy migration mechanisms, and uses a speculation mechanism that improves the efficiency of handling post-copy page faults. We modify the Linux kernel and develop a new page fault handler inside the guest OS to implement HSG-LM. Our experimental studies reveal that the technique reduces the downtime by as much as 55%, and reduces the total migration time by as much as 27% over competitors including Xen-based pre-copy, post-copy, and self-migration mechanisms. In a virtual cluster environment, one of the main challenges is to ensure equal utilization of all the available resources while avoiding overloading a subset of machines. We propose an efficient load balancing strategy using VM live migration, called DCbalance. Differently from previous work, DCbalance records the history of mappings to inform future placement decisions, and uses a workload-adaptive live migration algorithm to minimize VM downtime. We improve Xen's original live migration mechanism and implement the DCbalance technique, and conduct experimental studies. Our results reveal that DCbalance reduces the decision generating time by 79%, the downtime by 73%, and the total migration time by 38%, over competitors including the OSVD virtual machine load balancing mechanism and the DLB (Xen-based) dynamic load balancing algorithm. The dissertation's final contribution is a technique for VM live migration in Wide Area Networks (WANs), called FDM. In contrast to live migration in Local Area Networks (LANs), VM migration in WANs involve migrating disk data, besides memory state, because the source and the target machines do not share the same disk service. FDM is a fast and storage-adaptive migration mechanism that transmits both memory state and disk data with short downtime and total migration time. FDM uses page cache to identify data that is duplicated between memory and disk, so as to avoid transmitting the same data unnecessarily. We implement FDM in Xen, targeting different disk formats including raw and Qcow2. Our experimental studies reveal that FDM reduces the downtime by as much as 87%, and reduces the total migration time by as much as 58% over competitors including pre-copy or post-copy disk migration mechanisms and the disk migration mechanism implemented in BlobSeer, a widely used large-scale distributed storage service. / Ph. D.

Multidisciplinary design optimization (MDO) for large-scale engineering problems poses many challenges (e.g., the design of an efficient concurrent paradigm for global optimization based on disciplinary analyses, expensive computations over vast data sets, etc.) This work focuses on the application of distributed schemes for massively parallel architectures to MDO problems, as a tool for reducing computation time and solving larger problems. The specific problem considered here is configuration optimization of a high speed civil transport (HSCT), and the efficient parallelization of the embedded paradigm for reasonable design space identification. Two distributed dynamic load balancing techniques (random polling and global round robin with message combining) and two necessary termination detection schemes (global task count and token passing) were implemented and evaluated in terms of effectiveness and scalability to large problem sizes and a thousand processors. The effect of certain parameters on execution time was also inspected. Empirical results demonstrated stable performance and effectiveness for all schemes, and the parametric study showed that the selected algorithmic parameters have a negligible effect on performance. / Master of Science

In the last two-decades data center networks have evolved to become a key element in improving levels of productivity and competitiveness for different types of organizations. Traditionally data center networks have been constructed with 3 layers of switches, Edge, Aggregation, and Core. Although this Three-Tier architecture has worked well in the past, it poses a number of challenges for current and future data centers. Data centers today have evolved to support dynamic resources such as virtual machines and storage volumes from any physical location within the data center. This has led to highly volatile and unpredictable traffic patterns. Also The emergence of "Big Data" applications that exchange large volumes of information have created large persistent flows that need to coexist with other traffic flows. The Three-Tier architecture and current routing schemes are no longer sufficient for achieving high bandwidth utilization. Data center networks should be built in a way where they can adequately support virtualization and cloud computing technologies. Data center networks should provide services such as, simplified provisioning, workload mobility, dynamic routing and load balancing, equidistant bandwidth and latency. As data center networks have evolved the Three-Tier architecture has proven to be a challenge not only in terms of complexity and cost, but it also falls short of supporting many new data center applications. In this work we propose OneSwitch: A switch architecture for the data center. OneSwitch is backward compatible with current Ethernet standards and uses an OpenFlow central controller, a Location Database, a DHCP Server, and a Routing Service to build an Ethernet fabric that appears as one switch to end devices. This allows the data center to use switches in scale-out topologies to support hosts in a plug and play manner as well as provide much needed services such as dynamic load balancing, intelligent routing, seamless mobility, equidistant bandwidth and latency. / PHD

An accelerated pace of discovery in biological sciences is made possible by a new generation of computational biology and bioinformatics tools. In this dissertation we develop novel computational, analytical, and high performance simulation techniques for biological problems, with applications to the yeast cell division cycle, and to the RNA-Sequencing of the yellow fever mosquito. Cell cycle system evolves stochastic effects when there are a small number of molecules react each other. Consequently, the stochastic effects of the cell cycle are important, and the evolution of cells is best described statistically. Stochastic simulation algorithm (SSA), the standard stochastic method for chemical kinetics, is often slow because it accounts for every individual reaction event. This work develops a stochastic version of a deterministic cell cycle model, in order to capture the stochastic aspects of the evolution of the budding yeast wild-type and mutant strain cells. In order to efficiently run large ensembles to compute statistics of cell evolution, the dissertation investigates parallel simulation strategies, and presents a new probabilistic framework to analyze the performance of dynamic load balancing algorithms. This work also proposes new accelerated stochastic simulation algorithms based on a fully implicit approach and on stochastic Taylor expansions. Next Generation RNA-Sequencing, a high-throughput technology to sequence cDNA in order to get information about a sample's RNA content, is becoming an efficient genomic approach to uncover new genes and to study gene expression and alternative splicing. This dissertation develops efficient algorithms and strategies to find new genes in Aedes aegypti, which is the most important vector of dengue fever and yellow fever. We report the discovery of a large number of new gene transcripts, and the identification and characterization of genes that showed male-biased expression profiles. This basic information may open important avenues to control mosquito borne infectious diseases. / Ph. D.

The rapid advancement of Machine Learning (ML) and Deep Learning (DL) has revolutionized various domains, necessitating efficient and cost-effective ML inference capabilities. Function-as-a-Service (FaaS) has emerged as a promising approach for hosting ML inference services, providing a serverless computing environment that streamlines development cycles and offers scalability and simplified infrastructure management. However, existing autoscaling strategies employed by popular FaaS platforms often overlook critical factors such as response time and tail latency. Additionally, Python's Global Interpreter Lock (GIL) poses challenges for parallel computing in high-request traffic scenarios. This thesis addresses the need for efficient and cost-effective Machine Learning (ML) inference capabilities by exploring batching and autoscaling strategies for Serverless Inference instances. The study proposes a prototype FaaS framework that provides adaptive request batching, reactive autoscaling policies, and SLO monitoring, thus allowing Serverless Inference workloads to meet their SLO targets even during peak traffic. The proposed approach aims to optimize resource utilization, mitigate tail latency, and improve overall system performance. / Master of Science / Machine Learning (ML) and Deep Learning (DL) are advanced techniques that allow computers to learn from data and make predictions or decisions without being explicitly programmed. This has led to significant advancements in various fields. Inference refers to the process of applying a trained ML model to new data to make predictions or extract insights. In the context of ML, there is a growing need for efficient and cost-effective inference capabilities. A new approach called Function-as-a-Service (FaaS) has emerged that can address this need. FaaS is a way of abstracting the server infrastructure away from the developers. This means developers can focus on writing the ML code without worrying about managing the underlying infrastructure. FaaS offers benefits such as scalability, simplified infrastructure management, and faster development cycles. However, existing FaaS platforms face challenges in ensuring fast response times and handling high levels of incoming requests. This thesis aims to address these challenges by proposing a prototype FaaS framework. The framework incorporates adaptive request batching, reactive autoscaling policies, and Service-Level Objectives (SLOs) monitoring. Request batching allows the framework to process multiple requests together, improving efficiency. Autoscaling policies ensure the system dynamically adjusts its resources based on the incoming workload. Monitoring SLOs helps track and meet performance targets, even during peak traffic. By optimizing resource utilization, reducing delays in processing requests, and improving overall system performance, the proposed approach seeks to provide efficient and cost-effective ML inference capabilities in a serverless environment.