gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

One of the important questions in biological evolution is to know if certain changes along protein coding genes have contributed to the adaptation of species. This problem is known to be biologically complex and computationally very expensive. It, therefore, requires efficient Grid or cluster solutions to overcome the computational challenge. We have developed a Grid-enabled tool (gcodeml) that relies on the PAML (codeml) package to help analyse large phylogenetic datasets on both Grids and computational clusters. Although we report on results for gcodeml, our approach is applicable and customisable to related problems in biology or other scientific domains.Comment: 10 pages, 4 figures. To appear in the HealthGrid 2012 con

The Virginia Tech Computational Grid: A Research Agenda

An important goal of grid computing is to apply the rapidly expanding power of distributed computing resources to large-scale multidisciplinary scientic problem solving. Developing a usable computational grid for Virginia Tech is desirable from many perspectives. It leverages distinctive strengths of the university, can help meet the research computing needs of users with the highest demands, and will generate many challenging computer science research questions. By deploying a campus-wide grid and demonstrating its effectiveness for real applications, the Grid Computing Research Group hopes to gain valuable experience and contribute to the grid computing community. This report describes the needs and advantages which characterize the Virginia Tech context with respect to grid computing, and summarizes several current research projects which will meet those needs

A method of evaluation of high-performance computing batch schedulers

According to Sterling et al., a batch scheduler, also called workload management, is an application or set of services that provide a method to monitor and manage the flow of work through the system [Sterling01]. The purpose of this research was to develop a method to assess the execution speed of workloads that are submitted to a batch scheduler. While previous research exists, this research is different in that more complex jobs were devised that fully exercised the scheduler with established benchmarks. This research is important because the reduction of latency even if it is miniscule can lead to massive savings of electricity, time, and money over the long term. This is especially important in the era of green computing [Reuther18]. The methodology used to assess these schedulers involved the execution of custom automation scripts. These custom scripts were developed as part of this research to automatically submit custom jobs to the schedulers, take measurements, and record the results. There were multiple experiments conducted throughout the course of the research. These experiments were designed to apply the methodology and assess the execution speed of a small selection of batch schedulers. Due to time constraints, the research was limited to four schedulers. x The measurements that were taken during the experiments were wall time, RAM usage, and CPU usage. These measurements captured the utilization of system resources of each of the schedulers. The custom scripts were executed using, 1, 2, and 4 servers to determine how well a scheduler scales with network growth. The experiments were conducted on local school resources. All hardware was similar and was co-located within the same data-center. While the schedulers that were investigated as part of the experiments are agnostic to whether the system is grid, cluster, or super-computer; the investigation was limited to a cluster architecture

A .net based resource sharing framework

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2006.Includes bibliographical references (p. 121-124).This thesis presents an Internet resource sharing architecture. It allows users to access and utilize unused computer resources, such as CPU cycles and storage, without an expert's knowledge. It achieves this by providing a number of abstract services that hide some of the complexity inherent in distributed computing. In recent years, Grid Computing has been proposed as a solution for Internet resource sharing. However, Grid Computing as presently implemented does not address the need of the large majority of the users. In this thesis, we propose a different approach to achieve Internet resource sharing called the Realm. The Realm Framework offers a lightweight layer on top of the Microsoft .Net Framework so that the programs that can be migrated to .Net Framework can also utilize the shared resources through the Realm Framework. By leveraging the Microsoft .Net Framework, the Realm Framework avoids tedious re-working in this fast-paced world of technology by sitting on the top of the full-featured, coherent and up-to-date development platform. The Realm Framework applies current technologies such as Web Services, the Common Language Runtime (CLR) and popular encryption algorithms.(cont.) In this thesis a versatile runtime system and a set of extension interfaces in C# programming language is developed. The modularized software package offers a layered programming model for distributed-application developers with different levels of proficiency. Two utilities that are helpful for maintaining a distributed system are also developed, namely, a dynamic domain-name based inter-realm communication scheme and a distributed debugger. Examples of applying the Realm Framework to several typical scenarios are shown, including embarrassingly parallel problems that require little communication between computing nodes, parallel computing problems that require intensive message-passing between the computing nodes, and universal storage systems that are based on storage media and the messenger-like applications that require a sophisticated communication scheme.by Xiaohan LinPh.D

HPC Cloud for Scientific and Business Applications: Taxonomy, Vision, and Research Challenges

High Performance Computing (HPC) clouds are becoming an alternative to on-premise clusters for executing scientific applications and business analytics services. Most research efforts in HPC cloud aim to understand the cost-benefit of moving resource-intensive applications from on-premise environments to public cloud platforms. Industry trends show hybrid environments are the natural path to get the best of the on-premise and cloud resources---steady (and sensitive) workloads can run on on-premise resources and peak demand can leverage remote resources in a pay-as-you-go manner. Nevertheless, there are plenty of questions to be answered in HPC cloud, which range from how to extract the best performance of an unknown underlying platform to what services are essential to make its usage easier. Moreover, the discussion on the right pricing and contractual models to fit small and large users is relevant for the sustainability of HPC clouds. This paper brings a survey and taxonomy of efforts in HPC cloud and a vision on what we believe is ahead of us, including a set of research challenges that, once tackled, can help advance businesses and scientific discoveries. This becomes particularly relevant due to the fast increasing wave of new HPC applications coming from big data and artificial intelligence.Comment: 29 pages, 5 figures, Published in ACM Computing Surveys (CSUR

Experimental Study of Remote Job Submission and Execution on LRM through Grid Computing Mechanisms

Remote job submission and execution is fundamental requirement of distributed computing done using Cluster computing. However, Cluster computing limits usage within a single organization. Grid computing environment can allow use of resources for remote job execution that are available in other organizations. This paper discusses concepts of batch-job execution using LRM and using Grid. The paper discusses two ways of preparing test Grid computing environment that we use for experimental testing of concepts. This paper presents experimental testing of remote job submission and execution mechanisms through LRM specific way and Grid computing ways. Moreover, the paper also discusses various problems faced while working with Grid computing environment and discusses their trouble-shootings. The understanding and experimental testing presented in this paper would become very useful to researchers who are new to the field of job management in Grid.Comment: Fourth International Conference on Advanced Computing & Communication Technologies (ACCT), 201

Libra: An Economy driven Job Scheduling System for Clusters

Clusters of computers have emerged as mainstream parallel and distributed platforms for high-performance, high-throughput and high-availability computing. To enable effective resource management on clusters, numerous cluster managements systems and schedulers have been designed. However, their focus has essentially been on maximizing CPU performance, but not on improving the value of utility delivered to the user and quality of services. This paper presents a new computational economy driven scheduling system called Libra, which has been designed to support allocation of resources based on the users? quality of service (QoS) requirements. It is intended to work as an add-on to the existing queuing and resource management system. The first version has been implemented as a plugin scheduler to the PBS (Portable Batch System) system. The scheduler offers market-based economy driven service for managing batch jobs on clusters by scheduling CPU time according to user utility as determined by their budget and deadline rather than system performance considerations. The Libra scheduler ensures that both these constraints are met within an O(n) run-time. The Libra scheduler has been simulated using the GridSim toolkit to carry out a detailed performance analysis. Results show that the deadline and budget based proportional resource allocation strategy improves the utility of the system and user satisfaction as compared to system-centric scheduling strategies.Comment: 13 page