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In 2012, when Professor Shi introduced me to the concept of Statistic Multiplexed Computing (SMC), I was skeptical. It contradicted everything I have learned and heard about distributed and parallel computing. However, I did believe that unhandled failures in any application will negatively impact its scalability. For that, I agreed to take on the feasibility study of SMC for practical applications. After six+ years research and experimentations, it became clear to me that the most widely believed misconception is “either performance or reliability” when upscaling a distributed application. This conception was the result of the direct use of hop-by-hop communication protocols in distributed application construction. Terminology: Hop-by-hop data protocol is a two-sided reliable lossless data communication protocol for transmitting data between a sender and a receiver. Either the sender or the receiver crash will cause data losses. Examples: MPI, RPC, RMI, OpenMP. End-to-end data protocol is a single-sided reliable lossless data communication protocol for transmitting data between application programs. All runtime available processors, networks and storage will be automatically dispatched to the best effort support of the reliable communication regardless transient and permanent device failures. Examples: HDFS, Blockchain, Fabric and SMC. Active end-to-end data protocol is a single-sided reliable lossless data communication pro- tocol for transmitting data and automatically synchronizing application programs. Example: SMC (AnkaCom, AnkaStore (this dissertation)). Unlike the hop-by-hop protocols, the use of end-to-end protocol forms an application- dependent overlay network. An overlay network for distributed and parallel computing application, such as Blockchain, has been proven to defy the “common wisdom” for two important distributed computing challenges: a) Extreme scale computing without single-point failures is practically feasible. Thus, all transaction or data losses can be eliminated. b) Extreme scale synchronized transaction replication is practically feasible. Thus, the CAP conjecture and theorem become irrelevant. Unlike passive overlay networks, such as the HDFS and Blockchain, this dissertation study proves that an active overlay network can deliver higher performance, higher reliability and security at the same time as the application up scales. Although application-level security is not part of this dissertation, it is easy to see that application-level end-to-end protocols will fundamentally eliminate the “man-in-the-middle” attacks. This will nullify many well-known attacks. With the zero-single-point failure and zero impact synchronous replication features, SMC applications are naturally resistant to DDoS and ransomware attacks. This dissertation explores practical implementations of the SMC concept for compute intensive (CI) and data intensive (DI) applications. This defense will disclose the details of CI and DI runtime implementations and results of inductive computational experiments. The computational environments include the NSF Chameleon bare-metal HPC cloud and Temple’s TCloud cluster. / Computer and Information Science

System architecture analyses of distributed ship systems offer a practical view of system behavior over all operational states; however, the effectiveness of these analyses can be bound by limited computational performance or capability. Deactivation diagrams provide an alternative view to conventional system architecture descriptions, allowing for rapid analysis of system connectivity and flow based on precomputed single-state system descriptions. This thesis explores the development of system deactivation diagrams and their use in early-stage naval ship system design. Software tools developed in C++ and VBA as part of this research support the Virginia Tech (VT) Naval Ship Design Concept and Requirements Exploration (CandRE) process and tools utilizing the U.S. Navy's Leading-Edge Architecture for Prototyping Systems (LEAPS) framework database. These tools incorporate automated path-finding algorithms developed based on proven network theory and effective computational methods for use in performing ship system deactivation analysis. Data drawn from the results of this approach possess extensible applicability towards studies in naval ship system vulnerability, flow optimization, network architecture, and other system analyses. Supplementary work on interfacing the LEAPS framework libraries with deactivation analyses has demonstrated the capability for generating deactivation diagrams from complex LEAPS ship system databases and paved the way for future incorporation of LEAPS into research work at Virginia Tech. / Master of Science / As the development of new ships becomes more technically complex due to the increased incorporation of redundant and interdependent ship systems, there is a greater need for advanced tools to support future ship system design. Ship operational capabilities rely on the resiliency of onboard systems in all situations, included damaged conditions, and require comprehensive design evaluation to identify weaknesses in system concepts. This thesis details the development of a computational approach to ship system analysis using precomputed deactivation diagrams for early-stage naval ship system design. Deactivation diagrams are a unique way of looking at the interconnectivity of system components and offer a consolidated view of complex network architecture to significantly simplify and accelerate subsequent analyses. Developments in computational algorithms for ship system connectivity presented in this thesis aid in the automated development of deactivation diagrams and support system flow and vulnerability analyses with particular regard to ongoing work on the Virginia Tech (VT) Naval Ship Design Concept and Requirements Exploration (C&RE) process. Additional thesis development work referencing the U.S. Navy’s Leading-Edge Architecture for Prototyping Systems (LEAPS) database framework has demonstrated the capability for generating deactivation diagrams from complex LEAPS ship system databases and paved the way for future incorporation of LEAPS into research work at VT.

The key goal in this work is to enable a flexible ground station that is not constrained to a particular mission or set of hardware. In addition, with the concepts and software produced in this thesis, it will play a significant role in educating engineers and students by providing critical infrastructure and a sandbox for ground station operations. Key pieces of software were developed in this work to create a flexible and robust software-defined ground station. Several digital transmission modes were developed in order to allow communication between the ground station and common amateur radio CubeSats and SmallSats. In order to handle distributed tasks and process at a ground station with multiple servers and controllers, a specialized actor framework was written in Python for ease of use. Actors have the ability to send messages to one another over a network, and they maintain their own memory in order to avoid synchronization problems that come with sharing memory. In addition to the software developed in this work, a novel Peer-to-Peer (P2P) protocol for a network of ground stations is proposed in order to increase coverage and access to spacecraft without requiring centralized server infrastructure. This protocol provides the method to scale the developed software architecture beyond a single ground station. Since the Virginia Tech Ground Station (VTGS) will have many concurrent processes running across multiple servers, it was necessary to apply the actor model in order to simplify the design of the system. The purpose of this thesis is to describe the developed software for the VTGS as well as the P2P protocol for a larger network of ground stations. There are three primary repositories: planck-dsp, gr-vtgs, and pystation. The planck-dsp library and gr-vtgs Out-of-tree (OOT) make up the primary digital signal processing and communications toolboxes, where GNU Radio serves as the scheduler for signal processing blocks used in flow graphs. The pystation module is the extensible software actor framework that connects various systems both locally and remotely. It is also responsible for scheduling and handling ground station requests. While the software was primarily created for the VTGS, it is general enough to apply to other ground station implementations. / Master of Science

On-line services already form an important part of modern life with an immense potential for growth. Most of these services are supported by transactional systems, which are backed by database management systems (DBMS) in many cases. Many on-line services use replication to ensure high-availability, fault tolerance and scalability. Replicated systems typically consist of different nodes running the service co-ordinated by a distributed algorithm which aims to drive all the nodes along the same sequence of states by providing a total order to their operations. Thus optimization of both local DBMS operations through concurrency control and the distributed algorithm driving replicated services can lead to enhancing the performance of the on-line services. Deferred Update Replication (DUR) is a well-known approach to design scalable replicated systems. In this method, the database is fully replicated on each distributed node. User threads perform transactions locally and optimistically before a total order is reached. DUR based systems find their best usage when remote transactions rarely conflict. Even in such scenarios, transactions may abort due to local contention on nodes. A generally adopted method to alleviate the local contention is to invoke a local certification phase to check if a transaction conflicts with other local transactions already completed. If so, the given transaction is aborted locally without burdening the ordering layer. However, this approach still results in many local aborts which significantly degrades the performance. The first main contribution of this thesis is PXDUR, a DUR based transactional system, which enhances the performance of DUR based systems by alleviating local contention and increasing the transaction commit rate. PXDUR alleviates local contention by allowing speculative forwarding of shared objects from locally committed transactions awaiting total order to running transactions. PXDUR allows transactions running in parallel to use speculative forwarding, thereby enabling the system to utilize the highly parallel multi-core platforms. PXDUR also enhances the performance by optimizing the transaction commit process. It allows the committing transactions to skip read-set validation when it is safe to do so. PXDUR achieves performance gains of an order of magnitude over closest competitors under favorable conditions. Transactions also form an important part of centralized DBMS, which tend to support multi-threaded access to utilize the highly parallel hardware platforms. The applications can be wrapped in transactions which can then access the DBMS as per the rules of concurrency control. This allows users to develop applications that can run on DBMSs without worrying about synchronization. texttt{Serializability} is the de-facto standard form of isolation required by transactions for many applications. The existing methods employed by DBMSs to enforce serializability employ explicit fine-grained locking. The eager-locking based approach is pessimistic and can be too conservative for many applications. The locking approach can severely limit the performance of DBMSs especially for scenarios with moderate to high contention. This leads to the second major contribution of this thesis is TSAsR, an adaptive transaction processing framework, which can be applied to DBMSs to improve performance. TSAsR allows the DBMS's internal synchronization to be more relaxed and enforces serializability through the processng of external meta-data in an optimistic manner. It does not require any changes in the application code and achieves orders of magnitude performance improvements for high and moderate contention cases. The replicated transaction processing systems require a distributed algorithm to keep the system consistent by ensuring that each node executes the same sequence of deterministic commands. These algorithms generally employ texttt{State Machine Replication (SMR)}. Enhancing the performance of such algorithms is a potential way to increase the performance of distributed systems. However, developing new SMR algorithms is limited in production settings because of the huge verification cost involved in proving their correctness. There are frameworks that allow easy specification of SMR algorithms and subsequent verification. However, algorithms implemented in such framework, give poor performance. This leads to the third major contribution of this thesis Verified JPaxos, a JPaxos based runtime system which can be integrated to an easy to verify I/O automaton based on Multipaxos protocol. Multipaxos is specified in Higher Order Logic (HOL) for ease of verification which is used to generates executable code representing the Multipaxos state changes (I/O Automaton). The runtime drives the HOL generated code and interacts with the service and network to create a fully functional replicated Multipaxos system. The runtime inherits its design from JPaxos along with some optimizations. It achieves significant improvement over a state-of-art SMR verification framework while still being comparable to the performance of non-verified systems. / Master of Science

This thesis presents Caesar, a novel multi-leader Generalized Consensus protocol for geographically replicated systems. Caesar is able to achieve near-perfect availability, provide high performance - low latency and high throughput compared to the existing state-of-the- art, and tolerate replica failures. Recently, a number of state-of-the-art consensus protocols that implement the Generalized Consensus definition have been proposed. However, the major limitation of these existing approaches is the significant performance degradation when application workload produces conflicting requests. Caesar's main goal is to overcome this limitation by changing the way a fast decision is taken: its ordering protocol does not reject a fast decision for a client request if a quorum of nodes reply with different dependency sets for that request. It only switches to a slow decision if there is no chance to agree on the proposed order for that request. Caesar is able to achieve this using a combination of wait condition and logical time stamping. The effectiveness of Caesar is demonstrated through an evaluation study performed on Amazon's EC2 infrastructure using 5 geo-replicated sites. Caesar outperforms other multi-leader (e.g., EPaxos) competitors by as much as 1.7x in presence of 30% conflicting requests, and single-leader (e.g., Multi-Paxos) by as much as 3.5x. The protocol is also resistant to heavy client loads unlike existing protocols. / Master of Science

Distributed Transactional Memory (DTM) is an emerging, alternative concurrency control model that aims to overcome the challenges of distributed-lock based synchronization. DTM employs transactions in order to guarantee consistency in a concurrent execution. When two or more transactions conflict, all but one need to be delayed or rolled back. Transactional Memory supports code composability by nesting transactions. Nesting how- ever can be used as a strategy to improve performance. The closed nesting model enables partial rollback by allowing a sub-transaction to abort without aborting its parent, thus reducing the amount of work that needs to be retried. In the open nesting model, sub- transactions can commit to the shared state independently of their parents. This reduces isolation and increases concurrency. Our first main contribution in this dissertation are two extensions to the existing Transac- tional Forwarding Algorithm (TFA). Our extensions are N-TFA and TFA-ON, and support closed nesting and open nesting, respectively. We additionally extend the existing SCORe algorithm with support for open nesting (we call the result SCORe-ON). We implement these algorithms in a Java DTM framework and evaluate them. This represents the first study of transaction nesting in the context of DTM, and contributes the first DTM implementation which supports closed nesting or open nesting. Closed nesting through our N-TFA implementation proved insufficient for any significant throughput improvements. It ran on average 2% faster than flat nesting, while performance for individual tests varied between 42% slowdown and 84% speedup. The workloads that benefit most from closed nesting are characterized by short transactions, with between two and five sub-transactions. Open nesting, as exemplified by our TFA-ON and SCORe-ON implementations, showed promising results. We determined performance improvement to be a trade-off between the overhead of additional commits and the fundamental conflict rate. For write-intensive, high- conflict workloads, open nesting may not be appropriate, and we observed a maximum speedup of 30%. On the other hand, for lower fundamental-conflict workloads, open nesting enabled speedups of up to 167% in our tests. In addition to the two nesting algorithms, we also develop Hyflow2, a high-performance DTM framework for the Java Virtual Machine, written in Scala. It has a clean Scala API and a compatibility Java API. Hyflow2 was on average two times faster than Hyflow on high-contention workloads, and up to 16 times faster in low-contention workloads. Our second main contribution for improving DTM performance is automated data partition- ing. Modern transactional processing systems need to be fast and scalable, but this means many such systems settled for weak consistency models. It is however possible to achieve all of strong consistency, high scalability and high performance, by using fine-grained partitions and light-weight concurrency control that avoids superfluous synchronization and other over- heads such as lock management. Independent transactions are one such mechanism, that rely on good partitions and appropriately defined transactions. On the downside, it is not usually straightforward to determine optimal partitioning schemes, especially when dealing with non-trivial amounts of data. Our work attempts to solve this problem by automating the partitioning process, choosing the correct transactional primitive, and routing transactions appropriately. Our third main contribution is Alvin, a system for managing concurrently running trans- actions on a geographically replicated data-store. Alvin supports general-purpose transactions, and guarantees strong consistency criteria. Through a novel partial order broadcast protocol, Alvin maximizes the parallelism of ordering and local transaction processing, resulting in low client-perceived latency. Alvin can process read-only transactions either lo- cally or globally, according to the desired consistency criterion. Conflicting transactions are ordered across all sites. We built Alvin in the Go programming language. We conducted our evaluation study on Amazon EC2 infrastructure and compared against Paxos- and EPaxos- based state machine replication protocols. Our results reveal that Alvin provides significant speed-up for read-dominated TPC-C workloads: as much as 4.8x when compared to EPaxos on 7 datacenters, and up to 26% in write-intensive workloads. Our fourth and final contribution is M2Paxos, a multi-leader implementation of Generalized Consensus. Single leader-based consensus protocols are known to stop scaling once the leader reaches its saturation point. Ordering commands based on conflicts is appealing due to the potentially higher parallelism, but is imperfect due to the higher quorum sizes required for fast decisions and the need to compare commands and track their dependencies. M2Paxos on the other hand exploits fast decisions (i.e., delivery of a command in two communication delays) by leveraging a classic quorum size, matching a majority of nodes deployed. M2Paxos does not establish command dependencies based on conflicts, but it binds accessed objects to nodes, making sure commands operating on the same object will be ordered by the same node. Our evaluation study of M2Paxos (also built in Go) confirms the effectiveness of this approach, getting up to 7⨉ improvements in performance over state- of-the-art consensus and generalized consensus algorithms. / Ph. D.

Real-time Spatio-Temporal Analytics has become an integral part of Epidemiological studies. The size of the spatio-temporal data has been increasing tremendously over the years, gradually evolving into Big Data. The processing in such domains are highly data and compute intensive. High performance computing resources resources are actively being used to handle such workloads over massive datasets. This confluence of High performance computing and datasets with Big Data characteristics poses great challenges pertaining to data handling and processing. The resource management of supercomputers is in conflict with the data-intensive nature of spatio-temporal analytics. This is further exacerbated due to the fact that the data management is decoupled from the computing resources. Problems of these nature has provided great opportunities in the growth and development of tools and concepts centered around MapReduce based solutions. However, we believe that advanced relational concepts can still be employed to provide an effective solution to handle these issues and challenges. In this study, we explore distributed databases to efficiently handle spatio-temporal Big Data for epidemiological studies. We propose DiceX (Data Intensive Computational Epidemiology using supercomputers), which couples high-performance, Big Data and relational computing by embedding distributed data storage and processing engines within the supercomputer. It is characterized by scalable strategies for data ingestion, unified framework to setup and configure various processing engines, along with the ability to pause, materialize and restore images of a data session. In addition, we have successfully configured DiceX to support approximation algorithms from MADlib Analytics Library [54], primarily Count-Min Sketch or CM Sketch [33][34][35]. DiceX enables a new style of Big Data processing, which is centered around the use of clustered databases and exploits supercomputing resources. It can effectively exploit the cores, memory and compute nodes of supercomputers to scale processing of spatio-temporal queries on datasets of large volume. Thus, it provides a scalable and efficient tool for data management and processing of spatio-temporal data. Although DiceX has been designed for computational epidemiology, it can be easily extended to different data-intensive domains facing similar issues and challenges. We thank our external collaborators and members of the Network Dynamics and Simulation Science Laboratory (NDSSL) for their suggestions and comments. This work has been partially supported by DTRA CNIMS Contract HDTRA1-11-D-0016-0001, DTRA Validation Grant HDTRA1-11-1-0016, NSF - Network Science and Engineering Grant CNS-1011769, NIH and NIGMS - Models of Infectious Disease Agent Study Grant 5U01GM070694-11. Disclaimer: The views and conclusions contained herein are those of the authors and should not be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of the U.S. Government. / Master of Science