Grid warehousing of molecular dynamics protein unfolding data

With the increasing awareness of protein folding disorders, the explosion of genomic information, and the need for efficient ways to predict protein structure, protein folding and unfolding has become a central issue in molecular sciences research. Molecular dynamics computer simulations are increasingly employed to understand the folding and unfolding of proteins. Running protein unfolding simulations is computationally expensive and finding ways to enhance performance is a grid issue on its own. However, more and more groups run such simulations and generate a myriad of data, which raises new challenges in managing and analyzing these data. Because the vast range of proteins researchers want to study and simulate, the computational effort needed to generate data, the large data volumes involved, and the different types of analyses scientists need to perform, it is desirable to provide a public repository allowing researchers to pool and share protein unfolding data. This paper describes efforts to provide a grid-enabled data warehouse for protein unfolding data. We outline the challenge and present first results in the design and implementation of the data warehouse.

Statistical computations with AstroGrid and the Grid

We outline our first steps towards marrying two new and emerging technologies; the Virtual Observatory (e.g, Astro- Grid) and the computational grid. We discuss the construction of VOTechBroker, which is a modular software tool designed to abstract the tasks of submission and management of a large number of computational jobs to a distributed computer system. The broker will also interact with the AstroGrid workflow and MySpace environments. We present our planned usage of the VOTechBroker in computing a huge number of n–point correlation functions from the SDSS, as well as fitting over a million CMBfast models to the WMAP data.

Agents and the Grid: Service Discovery

The Grid is a large-scale computer system that is capable of coordinating resources that are not subject to centralised control, whilst using standard, open, general-purpose protocols and interfaces, and delivering non-trivial qualities of service. In this chapter, we argue that Grid applications very strongly suggest the use of agent-based computing, and we review key uses of agent technologies in Grids: user agents, able to customize and personalise data; agent communication languages offering a generic and portable communication medium; and negotiation allowing multiple distributed entities to reach service level agreements. In the second part of the chapter, we focus on Grid service discovery, which we have identified as a prime candidate for use of agent technologies: we show that Grid-services need to be located via personalised, semantic-rich discovery processes, which must rely on the storage of arbitrary metadata about services that originates from both service providers and service users. We present UDDI-MT, an extension to the standard UDDI service directory approach that supports the storage of such metadata via a tunnelling technique that ties the metadata store to the original UDDI directory. The outcome is a flexible service registry which is compatible with existing standards and also provides metadata-enhanced service discovery.

Performance of an operating high energy physics data grid: DOSAR-Grid

The DO experiment at Fermilab's Tevatron will record several petabytes of data over the next five years in pursuing the goals of understanding nature and searching for the origin of mass. Computing resources required to analyze these data far exceed capabilities of any one institution. Moreover, the widely scattered geographical distribution of DO collaborators poses further serious difficulties for optimal use of human and computing resources. These difficulties will exacerbate in future high energy physics experiments, like the LHC. The computing grid has long been recognized as a solution to these problems. This technology is being made a more immediate reality to end users in DO by developing a grid in the DO Southern Analysis Region (DOSAR), DOSAR-Grid, using a available resources within it and a home-grown local task manager, McFarm. We will present the architecture in which the DOSAR-Grid is implemented, the use of technology and the functionality of the grid, and the experience from operating the grid in simulation, reprocessing and data analyses for a currently running HEP experiment.

Performance analysis of smart grid communication protocol DNP3 over TCP/IP in a heterogeneous traffic environment

This paper presents simulation results of the DNP3 communication protocol over a TCP/IP network, for Smart Grid applications. The simulation was performed using the NS-2 network simulator. This study aimed to use the simulation to verify the performance of the DNP3 protocol in a heterogeneous LAN. Analyzing the results it was possible to verify that the DNP3 over a heterogeneous traffic network, with communication channel capacity between 60 and 85 percent, it works well with low packet loss and low delay, however, with traffic values upper 85 percent, the DNP3 usage becomes unfeasible because the information lost, re-transmissions and latency are significantly increased. © 2013 IEEE.

A NS-2 simulation model for DNP3 protocol over IEEE 802.15.4 wireless protocol toward low cost simulation of Smart Grid applications

Faced with an imminent restructuring of the electric power system, over the past few years many countries have invested in a new paradigm known as Smart Grid. This paradigm targets optimization and automation of electric power network, using advanced information and communication technologies. Among the main communication protocols for Smart Grids we have the DNP3 protocol, which provides secure data transmission with moderate rates. The IEEE 802.15.4 is another communication protocol also widely used in Smart Grid, especially in the so-called Home Area Network (HAN). Thus, many applications of Smart Grid depends on the interaction of these two protocols. This paper proposes modeling, in the traditional network simulator NS-2, the integration of DNP3 protocol and the IEEE 802.15.4 wireless standard for low cost simulations of Smart Grid applications.

Studi di data popularity nell'analisi distribuita su Grid dell'esperimento CMS a LHC

L’esperimento CMS a LHC ha raccolto ingenti moli di dati durante Run-1, e sta sfruttando il periodo di shutdown (LS1) per evolvere il proprio sistema di calcolo. Tra i possibili miglioramenti al sistema, emergono ampi margini di ottimizzazione nell’uso dello storage ai centri di calcolo di livello Tier-2, che rappresentano - in Worldwide LHC Computing Grid (WLCG)- il fulcro delle risorse dedicate all’analisi distribuita su Grid. In questa tesi viene affrontato uno studio della popolarità dei dati di CMS nell’analisi distribuita su Grid ai Tier-2. Obiettivo del lavoro è dotare il sistema di calcolo di CMS di un sistema per valutare sistematicamente l’ammontare di spazio disco scritto ma non acceduto ai centri Tier-2, contribuendo alla costruzione di un sistema evoluto di data management dinamico che sappia adattarsi elasticamente alle diversi condizioni operative - rimuovendo repliche dei dati non necessarie o aggiungendo repliche dei dati più “popolari” - e dunque, in ultima analisi, che possa aumentare l’“analysis throughput” complessivo. Il Capitolo 1 fornisce una panoramica dell’esperimento CMS a LHC. Il Capitolo 2 descrive il CMS Computing Model nelle sue generalità, focalizzando la sua attenzione principalmente sul data management e sulle infrastrutture ad esso connesse. Il Capitolo 3 descrive il CMS Popularity Service, fornendo una visione d’insieme sui servizi di data popularity già presenti in CMS prima dell’inizio di questo lavoro. Il Capitolo 4 descrive l’architettura del toolkit sviluppato per questa tesi, ponendo le basi per il Capitolo successivo. Il Capitolo 5 presenta e discute gli studi di data popularity condotti sui dati raccolti attraverso l’infrastruttura precedentemente sviluppata. L’appendice A raccoglie due esempi di codice creato per gestire il toolkit attra- verso cui si raccolgono ed elaborano i dati.

Elastic computing on Cloud resources for the CMS experiment

Nowadays, data handling and data analysis in High Energy Physics requires a vast amount of computational power and storage. In particular, the world-wide LHC Com- puting Grid (LCG), an infrastructure and pool of services developed and deployed by a ample community of physicists and computer scientists, has demonstrated to be a game changer in the efficiency of data analyses during Run-I at the LHC, playing a crucial role in the Higgs boson discovery. Recently, the Cloud computing paradigm is emerging and reaching a considerable adoption level by many different scientific organizations and not only. Cloud allows to access and utilize not-owned large computing resources shared among many scientific communities. Considering the challenging requirements of LHC physics in Run-II and beyond, the LHC computing community is interested in exploring Clouds and see whether they can provide a complementary approach - or even a valid alternative - to the existing technological solutions based on Grid. In the LHC community, several experiments have been adopting Cloud approaches, and in particular the experience of the CMS experiment is of relevance to this thesis. The LHC Run-II has just started, and Cloud-based solutions are already in production for CMS. However, other approaches of Cloud usage are being thought of and are at the prototype level, as the work done in this thesis. This effort is of paramount importance to be able to equip CMS with the capability to elastically and flexibly access and utilize the computing resources needed to face the challenges of Run-III and Run-IV. The main purpose of this thesis is to present forefront Cloud approaches that allow the CMS experiment to extend to on-demand resources dynamically allocated as needed. Moreover, a direct access to Cloud resources is presented as suitable use case to face up with the CMS experiment needs. Chapter 1 presents an overview of High Energy Physics at the LHC and of the CMS experience in Run-I, as well as preparation for Run-II. Chapter 2 describes the current CMS Computing Model, and Chapter 3 provides Cloud approaches pursued and used within the CMS Collaboration. Chapter 4 and Chapter 5 discuss the original and forefront work done in this thesis to develop and test working prototypes of elastic extensions of CMS computing resources on Clouds, and HEP Computing “as a Service”. The impact of such work on a benchmark CMS physics use-cases is also demonstrated.

Initializing a National Grid Infrastructure: Lessons Learned from the Swiss National Grid Association Seed Project

In addition to multi-national Grid infrastructures, several countries operate their own national Grid infrastructures to support science and industry within national borders. These infrastructures have the benefit of better satisfying the needs of local, regional and national user communities. Although Switzerland has strong research groups in several fields of distributed computing, only recently a national Grid effort was kick-started to integrate a truly heterogeneous set of resource providers, middleware pools, and users. In the following. article we discuss our efforts to start Grid activities at a national scale to combine several scientific communities and geographical domains. We make a strong case for the need of standards that have to be built on top of existing software systems in order to provide support for a heterogeneous Grid infrastruc

Code and readme of a MATLAB-based graphical user interface program for computing functionals of the geopotential

We present a novel graphical user interface program GrafLab (GRAvity Field LABoratory) for spherical harmonic synthesis (SHS) created in MATLAB®. This program allows to comfortably compute 38 various functionals of the geopotential up to ultra-high degrees and orders of spherical harmonic expansion. For the most difficult part of the SHS, namely the evaluation of the fully normalized associated Legendre functions (fnALFs), we used three different approaches according to required maximum degree: (i) the standard forward column method (up to maximum degree 1800, in some cases up to degree 2190); (ii) the modified forward column method combined with Horner's scheme (up to maximum degree 2700); (iii) the extended-range arithmetic (up to an arbitrary maximum degree). For the maximum degree 2190, the SHS with fnALFs evaluated using the extended-range arithmetic approach takes only approximately 2-3 times longer than its standard arithmetic counterpart, i.e. the standard forward column method. In the GrafLab, the functionals of the geopotential can be evaluated on a regular grid or point-wise, while the input coordinates can either be read from a data file or entered manually. For the computation on a regular grid we decided to apply the lumped coefficients approach due to significant time-efficiency of this method. Furthermore, if a full variance-covariance matrix of spherical harmonic coefficients is available, it is possible to compute the commission errors of the functionals. When computing on a regular grid, the output functionals or their commission errors may be depicted on a map using automatically selected cartographic projection.

An autonomic framework for enhancing the quality of data grid services

Data grid services have been used to deal with the increasing needs of applications in terms of data volume and throughput. The large scale, heterogeneity and dynamism of grid environments often make management and tuning of these data services very complex. Furthermore, current high-performance I/O approaches are characterized by their high complexity and specific features that usually require specialized administrator skills. Autonomic computing can help manage this complexity. The present paper describes an autonomic subsystem intended to provide self-management features aimed at efficiently reducing the I/O problem in a grid environment, thereby enhancing the quality of service (QoS) of data access and storage services in the grid. Our proposal takes into account that data produced in an I/O system is not usually immediately required. Therefore, performance improvements are related not only to current but also to any future I/O access, as the actual data access usually occurs later on. Nevertheless, the exact time of the next I/O operations is unknown. Thus, our approach proposes a long-term prediction designed to forecast the future workload of grid components. This enables the autonomic subsystem to determine the optimal data placement to improve both current and future I/O operations.

Using WYSIWYM to Create an Open-ended Interface for the Semantic Grid

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The impact of model detail on power grid resilience measures

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Fault-tolerant grid broadcasting /

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