A cost-benefit analysis of using cloud computing to extend the capacity of clusters

In this paper, we investigate the benefits that organisations can reap by using “Cloud Computing” providers to augment the computing capacity of their local infrastructure. We evaluate the cost of seven scheduling strategies used by an organisation that operates a cluster managed by virtual machine technology and seeks to utilise resources from a remote Infrastructure as a Service (IaaS) provider to reduce the response time of its user requests. Requests for virtual machines are submitted to the organisation’s cluster, but additional virtual machines are instantiated in the remote provider and added to the local cluster when there are insufficient resources to serve the users’ requests. Naïve scheduling strategies can have a great impact on the amount paid by the organisation for using the remote resources, potentially increasing the overall cost with the use of IaaS. Therefore, in this work we investigate seven scheduling strategies that consider the use of resources from the “Cloud”, to understand how these strategies achieve a balance between performance and usage cost, and how much they improve the requests’ response times.     

Security Implications of Typical Grid Computing Usage Scenarios

Grid Computing consists of a collection of heterogeneous computers and resources spread across multiple administrative domains with the intent of providing users uniform access to these resources. There are many ways to access the resources of a Grid, each with unique security requirements and implications for both the resource user and the resource provider. A comprehensive set of Grid usage scenarios is presented and analyzed with regard to security requirements such as authentication, authorization, integrity, and confidentiality. The main value of these scenarios and the associated security discussions is to provide a library of situations against which an application designer can match, thereby facilitating security-aware application use and development from the initial stages of the application design and invocation. A broader goal of these scenarios is to increase the awareness of security issues in Grid Computing.     

EGEETomo: a user-friendly, fault-tolerant and grid-enabled application for 3D reconstruction in electron tomography

Electron tomography is the leading technique to elucidate the structure of complex biological specimens. Due to the resolution needs, huge reconstructions are required. Grid computing has the potential to face the significant computational demands involved. However, there are a number of key issues, such as stability or difficult user-grid interaction, that currently preclude fully exploitation of its potential. EGEETomo is a user-friendly application that facilitates the interaction with the grid for the non-specialized user and automates job submission and supervision. In addition, EGEETomo is supplied with an automated fault recovery mechanism, which is key to make all the work transparent to the user. EGEETomo significantly accelerates tomographic reconstruction by exploiting the computational resources in the EGEE grid with minimal user intervention. AVAILABILITY: http://www.ace.ual.es/~jrbcast/EGEETomo.tar.gz     

An Ecosystem Model for Exploring Lake Restoration Effects on Fish Communities and Fisheries in Florida

Developing quantitative ecosystem–scale expectations of habitat restoration projects and examining trade‐offs associated with alternative approaches has been a challenge for restoration ecology. Many of the largest freshwater lake restoration projects have occurred in Florida to remediate degradation to vegetated littoral habitats resulting from stabilized water levels, but effects across lake food‐webs have not been assessed. We developed an ecosystem model using Ecopath with Ecosim and Ecospace for a generalized large, eutrophic Florida Lake to explore how simulated restoration activities could influence fish communities with emphasis on sport fish abundance. We modeled three habitat restoration scenarios: (1) “no control,” (2) a “10‐year control” that restored littoral habitat every 10 years, and (3) a “combined control” scenario that restored littoral habitat every 10 years with maintenance controls between 10‐year periods. Our “combined control” scenario provided the largest long‐term habitat restoration benefits for sport fish abundance and the fisheries they support. In Ecospace, we simulated a littoral habitat restoration project that reduced lake‐wide tussock coverage from 30 to 15%. Ecospace predicted positive benefits to sport fish and fisheries following the restoration simulation and highlighted the importance of habitat edge effects, spatial design of habitat restoration projects, and sampling designs for evaluating restoration projects.     

不同饵料对大口黑鲈生长性能和肠道微生物的影响

以冰鲜鱼、配合饲料和混合投喂3种饵料, 研究其对大口黑鲈(Micropterus salmoides)生长性能和肠道微生物的影响。结果表明, 在生长性能方面, 配合饲料组试验鱼的末均重、体长、增重率和特定生长率均显著低于冰鲜鱼组和混合投喂组(P<0.05), 混合投喂组最后养成规格最大, 生长速度也最快, 但与冰鲜鱼组差异不显著(P>0.05)。在肠道微生物群落的丰富度与多样性方面, 配合饲料投喂组丰富度最高, 冰鲜鱼组最低, 但冰鲜鱼组多样性最高, 配合饲料投喂组次之, 混合投喂组最低。在门级水平上, 厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)、放线菌门(Actinobacteriota)、蓝藻门(Cyanobacteria)、拟杆菌门(Bacteroidota)、浮霉菌门(Planctomycetota)、绿弯菌门(Chloroflexi)和酸杆菌门(Acidobacteriota)是大口黑鲈肠道优势菌群。属级水平上, 冰鲜鱼组的优势菌属主要为支原体属(Mycoplasma)、克雷伯氏菌属(Klebsiella)及聚球菌属(Synechococcus_CC9902); 配合饲料组优势菌属为克雷伯氏菌属(Klebsiella)、罗姆布茨菌(Romboutsia)及分枝杆菌属(Mycobacterium); 混合投喂组优势菌属则是支原体属(Mycoplasma)、厌氧氨氧化菌(Candidatus_Brocadia)及罗姆布茨菌(Romboutsia)。功能预测表明, 配合饲料投喂组大口黑鲈肠道菌群在“能量生产与转化”“碳水化合物运输和代谢”“氨基酸转运与代谢”和“脂质转运与代谢”等功能类群的相对丰度最高, 而冰鲜鱼组肠道菌群在“核苷酸的转运和代谢”“辅酶运输和代谢和翻译”“核糖体结构和生物发生”等功能类群的相对丰度占优。饵料对大口黑鲈的生长、肠道菌群组成和功能都具有显著的影响。研究为大口黑鲈的配合饲料开发和健康养殖提供了理论依据。     

Moral Distress and its Interconnection with Moral Sensitivity and Moral Resilience: Viewed from the Philosophy of Viktor E. Frankl

The interconnection between moral distress, moral sensitivity, and moral resilience was explored by constructing two hypothetical scenarios based on a recent Swedish newspaper report. In the first scenario, a 77-year-old man, rational and awake, was coded as “do not resuscitate” (DNR) against his daughter’s wishes. The patient died in the presence of nurses who were not permitted to resuscitate him. The second scenario concerned a 41-year-old man, who had been in a coma for three weeks. He was also coded as “do not resuscitate” and, when he stopped breathing, was resuscitated by his father. The nurses persuaded the physician on call to resume life support treatment and the patient recovered. These scenarios were analyzed using Viktor Frankl’s existential philosophy, resulting in a conceivable theoretical connection between moral distress, moral sensitivity, and moral resilience. To substantiate our conclusion, we encourage further empirical research.     

The Astrophysics Simulation Collaboratory: A Science Portal Enabling Community Software Development

Grid Portals, based on standard web technologies, are emerging as important and useful user interfaces to computational and data Grids. Grid Portals enable Virtual Organizations, comprised of distributed researchers to collaborate and access resources more efficiently and seamlessly. The Astrophysics Simulation Collaboratory (ASC) Grid Portal provides a framework to enable researchers in the field of numerical relativity to study astrophysical phenomenon by making use of the Cactus computational toolkit. We examine user requirements and describe the design and implementation of the ASC Grid Portal.     

Resource allocation mechanisms for maximizing provider’s revenue in infrastructure as a service (IaaS) cloud

Infrastructure as a Service (IaaS) is a cloud computing service provided over the internet to facilitate the provisioning of various services such as storage, processes, etc. The provider in the IaaS market may offer some purchasing plans including: reservation, on-demand, and spot plans for its resources. As in real scenarios, demand volume for each plan is assumed to be a random variable with a given probability distribution. The provider maximizes its average revenue in the long run by optimal allocation of its resources among the plans. We formulate an Integer Linear Programming (ILP) model with a stochastic constraint, to determine the number of resources to be allocated for each plan in every time slot in the planning horizon. First, fixed prices are considered for each plan, then two mechanisms of Continuous Double Auction and Second Price Sealed Bid Auction are considered for reservations and spot plans, respectively, to obtain market-driven prices of the services. The Seasonal Weighted Moving Average method is used to predict the amount of demand in every slot. Finally, the proposed mechanisms are evaluated through simulations and the results confirm the effectiveness of the methods in maximizing the revenue and overall utilization of the available IaaS capacity.

     

ABCGrid: Application for Bioinformatics Computing Grid

We have developed a package named Application for Bioinformatics Computing Grid (ABCGrid). ABCGrid was designed for biology laboratories to use heterogeneous computing resources and access bioinformatics applications from one master node. ABCGrid is very easy to install and maintain at the premise of robustness and high performance. We implement a mechanism to install and update all applications and databases in worker nodes automatically to reduce the workload of manual maintenance. We use a backup task method and self-adaptive job dispatch approach to improve performance. Currently, ABCGrid integrates NCBI_BLAST, Hmmpfam and CE, running on a number of computing platforms including UNIX/Linux, Windows and Mac OS X. AVAILABILITY: The source code, executables and documents can be downloaded from http://abcgrid.cbi.pku.edu.cn     

Harvesting for food versus feed: a review of Peruvian fisheries in a global context

Peru is the top exporter of fishmeal and fish oil (FMFO) worldwide and is responsible for half and a third of global production, respectively. Landings of “anchoveta” (Engraulis ringens) are used nearly exclusively for FMFO production, despite a proactive national food policy aimed at favoring the direct human consumption of this inexpensive species. It may be surprising that in a country where malnutrition and caloric deficit constitute major issues, a low-priced and highly nutritious fish such as anchovy does not have stronger domestic demand as a food fish. Here, we review and assess eight potential politico-socio-economic processes that can explain this situation. The main explanation are dietary habits, the preference for broiler and the higher profit from anchovy sold as feed fish compared to its use as a food fish due to historically high FMFO prices, boosted by an increasing demand for aquaculture in a context of finite forage and trash fish resources. In addition, the recent introduction of an individual quota system has shifted bargaining power from processors to fishers, thereby increasing competition for the raw material. This competition results in an increase in anchovy prices offered by the feed fish industry due to its onshore processing overcapacity, which is detrimental to the food fish industry. In the end, although the dominant use of anchovy for fish feed is largely explained by integrating these market mechanisms and other minor ones, this use raises other issues, such as rent redistribution through public policies, employment, equitability and utility (low social costs), and resource management (threats to ecosystems or global change). Different policy scenarios are proposed in relation to these issues.     

Ecological accounting for an integrated “pig–biogas–fish” system based on emergetic indicators

With the expansion of urbanization in China, the integrated biogas-utilization system has gained its popularity for both renewable energy production and multi-level utilization of organic waste. To appraise the ecological performance of the integrated biogas system, systematic accounting is undertaken for an integrated “pig–biogas–fish” system in Hubei province, China. Based on Odum's concept of embodied solar energy as a unified measure for environmental resources, human labors and purchased goods, a set of emergetic indicators are employed to quantify the system sustainability. The results reveal that in a 20-year designed lifetime scenario, 94.69% of the total emergy inputs for the “pig–biogas–fish” system are attributed to purchased social resources. Three kinds of products, namely pig, biogas, fish are taken into consideration, and transformity of the “pig–biogas–fish” system is calculated as 1.26E + 05 seJ/J. Compared with the Chinese conventional agriculture system, the integrated biogas system shows a higher sustainability. Given that most biogas systems have a lifespan less than 20 years, for the “pig–biogas–fish” system, six other scenarios with different lifespans are studied to investigate the impact of the lifespan on sustainability. The findings suggest that the “pig–biogas–fish” system should be well operated for at least 8 years to prove its advantage in ecological economy over the conventional agriculture system. This has essential policy implications that local government should strengthen subsequent management on biogas production to extend the practical service life of the biogas system.     

Cyberinfrastructure for the analysis of ecological acoustic sensor data: a use case study in grid deployment

The LTER Grid Pilot Study was conducted by the National Center for Supercomputing Applications, the University of New Mexico, and Michigan State University, to design and build a prototype grid for the ecological community. The featured grid application, the Biophony Grid Portal, manages acoustic data from field sensors and allows researchers to conduct real-time digital signal processing analysis on high-performance systems via a web-based portal. Important characteristics addressed during the study include the management, access, and analysis of a large set of field collected acoustic observations from microphone sensors, single signon, and data provenance. During the development phase of this project, new features were added to standard grid middleware software and have already been successfully leveraged by other, unrelated grid projects. This paper provides an overview of the Biophony Grid Portal application and requirements, discusses considerations regarding grid architecture and design, details the technical implementation, and summarizes key experiences and lessons learned that are generally applicable to all developers and administrators in a grid environment.     

Talisman--rapid application development for the grid

In order to make use of the emerging grid and network services offered by various institutes and mandated by many current research projects, some kind of user accessible client is required. In contrast with attempts to build generic workbenches, Talisman is designed to allow a bioinformatics expert to rapidly build custom applications, immediately visible using standard web technology, for users who wish to concentrate on the biology of their problem rather than the informatics aspects. As a component of the MyGrid project, it is intended to allow access to arbitrary resources, including but not limited to relational, object and flat file data sources, analysis programs and grid based storage, tracking and distributed annotation systems.     

SpeQuloS: a QoS service for hybrid and elastic computing infrastructures

The large choice of Distributed Computing Infrastructures (DCIs) available allows users to select and combine their preferred architectures amongst Clusters, Grids, Clouds, Desktop Grids and more. In these hybrid DCIs, elasticity is emerging as a key property. In elastic infrastructures, resources available to execute application continuously vary, either because of application requirements or because of constraints on the infrastructure, such as node volatility. In the former case, there is no guarantee that the computing resources will remain available during the entire execution of an application. In this paper, we show that Bag-of-Tasks (BoT) execution on these “Best-Effort” infrastructures suffer from a drop of the task completion rate at the end of the execution. The SpeQuloS service presented in this paper improves the Quality of Service (QoS) of BoT applications executed on hybrid and elastic infrastructures. SpeQuloS monitors the execution of the BoT, and dynamically supplies fast and reliable Cloud resources when the critical part of the BoT is executed. SpeQuloS offers several features to hybrid DCIs users, such as estimating completion time and execution speedup. Performance evaluation shows that BoT executions can be accelerated by a factor 2, while offloading less than 2.5 % of the workload to the Cloud. We report on several scenarios where SpeQuloS is deployed on hybrid infrastructures featuring a large variety of infrastructures combinations. In the context of the European Desktop Grid Initiative (EDGI), SpeQuloS is operated to improve QoS of Desktop Grids using resources from private Clouds. We present a use case where SpeQuloS uses both EC2 regular and spot instances to decrease the cost of computation while preserving a similar QoS level. Finally, in the last scenario SpeQuloS allows to optimize Grid5000 resources utilization.     

Personal adaptive clusters as containers for scientific jobs

We describe a system for creating personal clusters in user-space to support the submission and management of thousands of compute-intensive serial jobs to the network-connected compute resources on the NSF TeraGrid. The system implements a robust infrastructure that submits and manages job proxies across a distributed computing environment. These job proxies contribute resources to personal clusters created dynamically for a user on-demand. The personal clusters then adapt to the prevailing job load conditions at the distributed sites by migrating job proxies to sites expected to provide resources more quickly. Furthermore, the system allows multiple instances of these personal clusters to be created as containers for individual scientific experiments, allowing the submission environment to be customized for each instance. The version of the system described in this paper allows users to build large personal Condor and Sun Grid Engine clusters on the TeraGrid. Users then manage their scientific jobs, within each personal cluster, with a single uniform interface using the feature-rich functionality found in these job management environments.

Man-made lakes,ecological studies and conservation needs in Nigeria

The benefit derived from the creation of man-made lakes in Nigeria and other developing countries is usually associated with great risks. Whenever we establish a dam, it appears we dam the inherent consequences to the detriment of man and his environment. Debts were incurred by the countries concerned, man and animals were displaced, arable lands destroyed including degradation of forest and wild life resources. The creation of dams have also ignored the prevention of man and his life stock from the inherent spread of water borne diseases. The purpose for which a dam is created is threatened if man is indiscriminately exposed to the risk of water borne diseases. The poor and uneconomic management of the fish resources is also another major issue of concern. In order to tap the full potentials of reservoir projects and to promote conservation, it is important to have a round table talk involving all stake holders during the planning stage of such projects. Therefore apart from the engineering works, there is also need for collaboration with all experts from related fields especially the biologists, sociologists and economists for bio-socio-economic reasons during the planning and implementation stages of dam projects in Nigeria and other developing countries.     

A new approach to the job scheduling problem in computational grids

Job scheduling is one of the most challenging issues in Grid resource management that strongly affects the performance of the whole Grid environment. The major drawback of the existing Grid scheduling algorithms is that they are unable to adapt with the dynamicity of the resources and the network conditions. Furthermore, the network model that is used for resource information aggregation in most scheduling methods is centralized or semi-centralized. Therefore, these methods do not scale well as Grid size grows and do not perform well as the environmental conditions change with time. This paper proposes a learning automata-based job scheduling algorithm for Grids. In this method, the workload that is placed on each Grid node is proportional to its computational capacity and varies with time according to the Grid constraints. The performance of the proposed algorithm is evaluated through conducting several simulation experiments under different Grid scenarios. The obtained results are compared with those of several existing methods. Numerical results confirm the superiority of the proposed algorithm over the others in terms of makespan, flowtime, and load balancing.     

GLAD: a system for developing and deploying large-scale bioinformatics grid

MOTIVATION: Grid computing is used to solve large-scale bioinformatics problems with gigabytes database by distributing the computation across multiple platforms. Until now in developing bioinformatics grid applications, it is extremely tedious to design and implement the component algorithms and parallelization techniques for different classes of problems, and to access remotely located sequence database files of varying formats across the grid. In this study, we propose a grid programming toolkit, GLAD (Grid Life sciences Applications Developer), which facilitates the development and deployment of bioinformatics applications on a grid. RESULTS: GLAD has been developed using ALiCE (Adaptive scaLable Internet-based Computing Engine), a Java-based grid middleware, which exploits the task-based parallelism. Two bioinformatics benchmark applications, such as distributed sequence comparison and distributed progressive multiple sequence alignment, have been developed using GLAD.     

Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated compute and data grid

This paper describes a prototype grid infrastructure, called the “eMinerals minigrid”, for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers.     

Condor-G: A Computation Management Agent for Multi-Institutional Grids

In recent years, there has been a dramatic increase in the number of available computing and storage resources. Yet few tools exist that allow these resources to be exploited effectively in an aggregated form. We present the Condor-G system, which leverages software from Globus and Condor to enable users to harness multi-domain resources as if they all belong to one personal domain. We describe the structure of Condor-G and how it handles job management, resource selection, security, and fault tolerance. We also present results from application experiments with the Condor-G system. We assert that Condor-G can serve as a general-purpose interface to Grid resources, for use by both end users and higher-level program development tools.