Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Software-Defined Cloud Computing: Architectural Elements and Open Challenges

The variety of existing cloud services creates a challenge for service providers to enforce reasonable Software Level Agreements (SLA) stating the Quality of Service (QoS) and penalties in case QoS is not achieved. To avoid such penalties at the same time that the infrastructure operates with minimum energy and resource wastage, constant monitoring and adaptation of the infrastructure is needed. We refer to Software-Defined Cloud Computing, or simply Software-Defined Clouds (SDC), as an approach for automating the process of optimal cloud configuration by extending virtualization concept to all resources in a data center. An SDC enables easy reconfiguration and adaptation of physical resources in a cloud infrastructure, to better accommodate the demand on QoS through a software that can describe and manage various aspects comprising the cloud environment. In this paper, we present an architecture for SDCs on data centers with emphasis on mobile cloud applications. We present an evaluation, showcasing the potential of SDC in two use cases-QoS-aware bandwidth allocation and bandwidth-aware, energy-efficient VM placement-and discuss the research challenges and opportunities in this emerging area.Comment: Keynote Paper, 3rd International Conference on Advances in Computing, Communications and Informatics (ICACCI 2014), September 24-27, 2014, Delhi, Indi

Performance optimization of big data computing workflows for batch and stream data processing in multi-clouds

Workflow techniques have been widely used as a major computing solution in many science domains. With the rapid deployment of cloud infrastructures around the globe and the economic benefits of cloud-based computing and storage services, an increasing number of scientific workflows have migrated or are in active transition to clouds. As the scale of scientific applications continues to grow, it is now common to deploy various data- and network-intensive computing workflows such as serial computing workflows, MapReduce/Spark-based workflows, and Storm-based stream data processing workflows in multi-cloud environments, where inter-cloud data transfer oftentimes plays a significant role in both workflow performance and financial cost. Rigorous mathematical models are constructed to analyze the intra- and inter-cloud execution process of scientific workflows and a class of budget-constrained workflow mapping problems are formulated to optimize the network performance of big data workflows in multi-cloud environments. Research shows that these problems are all NP-complete and a heuristic solution is designed for each that takes into consideration module execution, data transfer, and I/O operations. The performance superiority of the proposed solutions over existing methods are illustrated through extensive simulations and further verified by real-life workflow experiments deployed in public clouds

Scientific Workflows for Metabolic Flux Analysis

Metabolic engineering is a highly interdisciplinary research domain that interfaces biology, mathematics, computer science, and engineering. Metabolic flux analysis with carbon tracer experiments (13 C-MFA) is a particularly challenging metabolic engineering application that consists of several tightly interwoven building blocks such as modeling, simulation, and experimental design. While several general-purpose workflow solutions have emerged in recent years to support the realization of complex scientific applications, the transferability of these approaches are only partially applicable to 13C-MFA workflows. While problems in other research fields (e.g., bioinformatics) are primarily centered around scientific data processing, 13C-MFA workflows have more in common with business workflows. For instance, many bioinformatics workflows are designed to identify, compare, and annotate genomic sequences by "pipelining" them through standard tools like BLAST. Typically, the next workflow task in the pipeline can be automatically determined by the outcome of the previous step. Five computational challenges have been identified in the endeavor of conducting 13 C-MFA studies: organization of heterogeneous data, standardization of processes and the unification of tools and data, interactive workflow steering, distributed computing, and service orientation. The outcome of this thesis is a scientific workflow framework (SWF) that is custom-tailored for the specific requirements of 13 C-MFA applications. The proposed approach – namely, designing the SWF as a collection of loosely-coupled modules that are glued together with web services – alleviates the realization of 13C-MFA workflows by offering several features. By design, existing tools are integrated into the SWF using web service interfaces and foreign programming language bindings (e.g., Java or Python). Although the attributes "easy-to-use" and "general-purpose" are rarely associated with distributed computing software, the presented use cases show that the proposed Hadoop MapReduce framework eases the deployment of computationally demanding simulations on cloud and cluster computing resources. An important building block for allowing interactive researcher-driven workflows is the ability to track all data that is needed to understand and reproduce a workflow. The standardization of 13 C-MFA studies using a folder structure template and the corresponding services and web interfaces improves the exchange of information for a group of researchers. Finally, several auxiliary tools are developed in the course of this work to complement the SWF modules, i.e., ranging from simple helper scripts to visualization or data conversion programs. This solution distinguishes itself from other scientific workflow approaches by offering a system of loosely-coupled components that are flexibly arranged to match the typical requirements in the metabolic engineering domain. Being a modern and service-oriented software framework, new applications are easily composed by reusing existing components

A Survey on Automatic Parameter Tuning for Big Data Processing Systems

Big data processing systems (e.g., Hadoop, Spark, Storm) contain a vast number of configuration parameters controlling parallelism, I/O behavior, memory settings, and compression. Improper parameter settings can cause significant performance degradation and stability issues. However, regular users and even expert administrators grapple with understanding and tuning them to achieve good performance. We investigate existing approaches on parameter tuning for both batch and stream data processing systems and classify them into six categories: rule-based, cost modeling, simulation-based, experiment-driven, machine learning, and adaptive tuning. We summarize the pros and cons of each approach and raise some open research problems for automatic parameter tuning.Peer reviewe