Replica maintenance strategy for data grid

Data Grid is an infrastructure that manages huge amount of data files, and provides intensive computational resources across geographically distributed collaboration.Increasing the performance of such system can be achieved by improving the overall resource usage, which includes network and storage resources.Improving network resource usage is achieved by good utilization of network bandwidth that is considered as an important factor affecting job execution time.Meanwhile, improving storage resource usage is achieved by good utilization of storage space usage. Data replication is one of the methods used to improve the performance of data access in distributed systems by replicating multiple copies of data files in the distributed sites.Having distributed the replicas to various locations, they need to be monitored.As a result of dynamic changes in the data grid environment, some of the replicas need to be relocated.In this paper we proposed a maintenance replica placement strategy termed as Unwanted Replica Deletion Strategy (URDS) as a part of Replica maintenance service.The main purpose of the proposed strategy is to find the placement of unwanted replicas to be deleted.OptorSim is used to evaluate the performance of the proposed strategy. The simulation results show that URDS requires less execution time and consumes less network usage and has a best utilization of storage space usage compared to existing approaches

Replica Creation Algorithm for Data Grids

Data grid system is a data management infrastructure that facilitates reliable access and sharing of large amount of data, storage resources, and data transfer services that can be scaled across distributed locations. This thesis presents a new replication algorithm that improves data access performance in data grids by distributing relevant data copies around the grid. The new Data Replica Creation Algorithm (DRCM) improves performance of data grid systems by reducing job execution time and making the best use of data grid resources (network bandwidth and storage space). Current algorithms focus on number of accesses in deciding which file to replicate and where to place them, which ignores resources’ capabilities. DRCM differs by considering both user and resource perspectives; strategically placing replicas at locations that provide the lowest transfer cost. The proposed algorithm uses three strategies: Replica Creation and Deletion Strategy (RCDS), Replica Placement Strategy (RPS), and Replica Replacement Strategy (RRS). DRCM was evaluated using network simulation (OptorSim) based on selected performance metrics (mean job execution time, efficient network usage, average storage usage, and computing element usage), scenarios, and topologies. Results revealed better job execution time with lower resource consumption than existing approaches. This research contributes replication strategies embodied in one algorithm that enhances data grid performance, capable of making a decision on creating or deleting more than one file during same decision. Furthermore, dependency-level-between-files criterion was utilized and integrated with the exponential growth/decay model to give an accurate file evaluation

An enhanced dynamic replica creation and eviction mechanism in data grid federation environment

Data Grid Federation system is an infrastructure that connects several grid systems, which facilitates sharing of large amount of data, as well as storage and computing resources. The existing mechanisms on data replication focus on finding file values based on the number of files access in deciding which file to replicate, and place new replicas on locations that provide minimum read cost. DRCEM finds file values based on logical dependencies in deciding which file to replicate, and allocates new replicas on locations that provide minimum replica placement cost. This thesis presents an enhanced data replication strategy known as Dynamic Replica Creation and Eviction Mechanism (DRCEM) that utilizes the usage of data grid resources, by allocating appropriate replica sites around the federation. The proposed mechanism uses three schemes: 1) Dynamic Replica Evaluation and Creation Scheme, 2) Replica Placement Scheme, and 3) Dynamic Replica Eviction Scheme. DRCEM was evaluated using OptorSim network simulator based on four performance metrics: 1) Jobs Completion Times, 2) Effective Network Usage, 3) Storage Element Usage, and 4) Computing Element Usage. DRCEM outperforms ELALW and DRCM mechanisms by 30% and 26%, in terms of Jobs Completion Times. In addition, DRCEM consumes less storage compared to ELALW and DRCM by 42% and 40%. However, DRCEM shows lower performance compared to existing mechanisms regarding Computing Element Usage, due to additional computations of files logical dependencies. Results revealed better jobs completion times with lower resource consumption than existing approaches. This research produces three replication schemes embodied in one mechanism that enhances the performance of Data Grid Federation environment. This has contributed to the enhancement of the existing mechanism, which is capable of deciding to either create or evict more than one file during a particular time. Furthermore, files logical dependencies were integrated into the replica creation scheme to evaluate data files more accurately

Cloud Storage and Bioinformatics in a private cloud deployment: Lessons for Data Intensive research

This paper describes service portability for a private cloud deployment, including a detailed case study about Cloud Storage and bioinformatics services developed as part of the Cloud Computing Adoption Framework (CCAF). Our Cloud Storage design and deployment is based on Storage Area Network (SAN) technologies, details of which include functionalities, technical implementation, architecture and user support. Experiments for data services (backup automation, data recovery and data migration) are performed and results confirm backup automation is completed swiftly and is reliable for data-intensive research. The data recovery result confirms that execution time is in proportion to quantity of recovered data, but the failure rate increases in an exponential manner. The data migration result confirms execution time is in proportion to disk volume of migrated data, but again the failure rate increases in an exponential manner. In addition, benefits of CCAF are illustrated using several bioinformatics examples such as tumour modelling, brain imaging, insulin molecules and simulations for medical training. Our Cloud Storage solution described here offers cost reduction, time-saving and user friendliness

Preliminary specification and design documentation for software components to achieve catallaxy in computational systems

This Report is about the preliminary specifications and design documentation for software components to achieve Catallaxy in computational systems. -- Die Arbeit beschreibt die Spezifikation und das Design von Softwarekomponenten, um das Konzept der Katallaxie in Grid Systemen umzusetzen. Eine Einführung ordnet das Konzept der Katallaxie in bestehende Grid Taxonomien ein und stellt grundlegende Komponenten vor. Anschließend werden diese Komponenten auf ihre Anwendbarkeit in bestehenden Application Layer Netzwerken untersucht.Grid Computing

Simulator adaptation at runtime for component-based simulation software

Component-based simulation software can provide many opportunities to compose and configure simulators, resulting in an algorithm selection problem for the user of this software. This thesis aims to automate the selection and adaptation of simulators at runtime in an application-independent manner. Further, it explores the potential of tailored and approximate simulators - in this thesis concretely developed for the modeling language ML-Rules - supporting the effectiveness of the adaptation scheme.Komponenten-basierte Simulationssoftware kann viele Möglichkeiten zur Komposition und Konfiguration von Simulatoren bieten und damit zu einem Konfigurationsproblem für Nutzer dieser Software führen. Das Ziel dieser Arbeit ist die Entwicklung einer generischen und automatisierten Auswahl- und Adaptionsmethode für Simulatoren. Darüber hinaus wird das Potential von spezifischen und approximativen Simulatoren anhand der Modellierungssprache ML-Rules untersucht, welche die Effektivität des entwickelten Adaptionsmechanismus erhöhen können

Prediction of protein-protein interaction sites using an ensemble method

<p>Abstract</p> <p>Background</p> <p>Prediction of protein-protein interaction sites is one of the most challenging and intriguing problems in the field of computational biology. Although much progress has been achieved by using various machine learning methods and a variety of available features, the problem is still far from being solved.</p> <p>Results</p> <p>In this paper, an ensemble method is proposed, which combines bootstrap resampling technique, SVM-based fusion classifiers and weighted voting strategy, to overcome the imbalanced problem and effectively utilize a wide variety of features. We evaluate the ensemble classifier using a dataset extracted from 99 polypeptide chains with 10-fold cross validation, and get a AUC score of 0.86, with a sensitivity of 0.76 and a specificity of 0.78, which are better than that of the existing methods. To improve the usefulness of the proposed method, two special ensemble classifiers are designed to handle the cases of missing homologues and structural information respectively, and the performance is still encouraging. The robustness of the ensemble method is also evaluated by effectively classifying interaction sites from surface residues as well as from all residues in proteins. Moreover, we demonstrate the applicability of the proposed method to identify interaction sites from the non-structural proteins (NS) of the influenza A virus, which may be utilized as potential drug target sites.</p> <p>Conclusion</p> <p>Our experimental results show that the ensemble classifiers are quite effective in predicting protein interaction sites. The Sub-EnClassifiers with resampling technique can alleviate the imbalanced problem and the combination of Sub-EnClassifiers with a wide variety of feature groups can significantly improve prediction performance.</p