TY - RPRT T1 - The Implementation of OpenStack Cinder and Integration with NetApp and Ceph Y1 - 2013 A1 - Gary McGilvary A1 - Thomas Oulevey AB - With the ever increasing amount of data produced from Large Hadron Collider (LHC) experiments, new ways are sought to help analyze and store this data as well as help researchers perform their own experiments. To help offer solutions to such problems, CERN has employed the use of cloud computing and in particular OpenStack; an open source and scalable platform for building public and private clouds. The OpenStack project contains many components such as Cinder used to create block storage that can be attached to virtual machines and in turn help increase performance. However instead of creating volumes locally with OpenStack, others remote storage clusters exist offering block based storage with features not present in the current OpenStack implementation; two popular solutions are NetApp and Ceph. Two features Ceph offers is the ability to stripe data stored within volumes over the distributed cluster as well as locally cache this data, both with the aim of improving performance. When in use with OpenStack, Ceph performs default data striping where the number and size of stripes is fixed and cannot be changed dependent on the volume to be created. Similarly, Ceph does not perform data caching when integrated with OpenStack. In this project we outline and document the integration of NetApp and Ceph with OpenStack as well as benchmark the performance of the NetApp and Ceph clusters already present at CERN. To allow Ceph data striping, we modify OpenStack to take the number and size of stripes input via the user to create volumes whose data is then striped according to the values they specify. Similarly, we also modify OpenStack to enable Ceph caching and allow users to select the caching policy they require per-volume. In this report, we describe how these features are implemented. JF - CERN Openlab PB - CERN ER - TY - Generic T1 - HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences Y1 - 2012 ED - Gesing, Sandra ED - Glatard, Tristan ED - Krüger, Jens ED - Delgado Olabarriaga, Silvia ED - Solomonides, Tony ED - Silverstein, J. ED - Montagnat, J. ED - Gaignard, A. ED - Krefting, Dagmar PB - IOS Press VL - 175 ER - TY - JOUR T1 - Performance database: capturing data for optimizing distributed streaming workflows JF - Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences Y1 - 2011 A1 - Chee Sun Liew A1 - Atkinson, Malcolm P. A1 - Radoslaw Ostrowski A1 - Murray Cole A1 - van Hemert, Jano I. A1 - Liangxiu Han KW - measurement framework KW - performance data KW - streaming workflows AB - The performance database (PDB) stores performance-related data gathered during workflow enactment. We argue that by carefully understanding and manipulating this data, we can improve efficiency when enacting workflows. This paper describes the rationale behind the PDB, and proposes a systematic way to implement it. The prototype is built as part of the Advanced Data Mining and Integration Research for Europe project. We use workflows from real-world experiments to demonstrate the usage of PDB. VL - 369 IS - 1949 ER - TY - JOUR T1 - Simultaneous alignment of short reads against multiple genomes JF - Genome Biol Y1 - 2009 A1 - Schneeberger, Korbinian A1 - Hagmann, Jörg A1 - Ossowski, Stephan A1 - Warthmann, Norman A1 - Gesing, Sandra A1 - Kohlbacher, Oliver A1 - Weigel, Detlef VL - 10 UR - http://www.biomedsearch.com/nih/Simultaneous-alignment-short-reads-against/19761611.html ER - TY - JOUR T1 - A Strategy for Research and Innovation in the Century of Information JF - Prometheus Y1 - 2009 A1 - e-Science Directors’ Forum Strategy Working Group A1 - Atkinson, M. A1 - Britton, D. A1 - Coveney, P. A1 - De Roure, D A1 - Garnett, N. A1 - Geddes, N. A1 - Gurney, R. A1 - Haines, K. A1 - Hughes, L. A1 - Ingram, D. A1 - Jeffreys, P. A1 - Lyon, L. A1 - Osborne, I. A1 - Perrott, P. A1 - Procter. R. A1 - Rusbridge, C. AB - More data will be produced in the next five years than in the entire history of human kind, a digital deluge that marks the beginning of the Century of Information. Through a year‐long consultation with UK researchers, a coherent strategy has been developed, which will nurture Century‐of‐Information Research (CIR); it crystallises the ideas developed by the e‐Science Directors’ Forum Strategy Working Group. This paper is an abridged version of their latest report which can be found at: http://wikis.nesc.ac.uk/escienvoy/Century_of_Information_Research_Strategy which also records the consultation process and the affiliations of the authors. This document is derived from a paper presented at the Oxford e‐Research Conference 2008 and takes into account suggestions made in the ensuing panel discussion. The goals of the CIR Strategy are to facilitate the growth of UK research and innovation that is data and computationally intensive and to develop a new culture of ‘digital‐systems judgement’ that will equip research communities, businesses, government and society as a whole, with the skills essential to compete and prosper in the Century of Information. The CIR Strategy identifies a national requirement for a balanced programme of coordination, research, infrastructure, translational investment and education to empower UK researchers, industry, government and society. The Strategy is designed to deliver an environment which meets the needs of UK researchers so that they can respond agilely to challenges, can create knowledge and skills, and can lead new kinds of research. It is a call to action for those engaged in research, those providing data and computational facilities, those governing research and those shaping education policies. The ultimate aim is to help researchers strengthen the international competitiveness of the UK research base and increase its contribution to the economy. The objectives of the Strategy are to better enable UK researchers across all disciplines to contribute world‐leading fundamental research; to accelerate the translation of research into practice; and to develop improved capabilities, facilities and context for research and innovation. It envisages a culture that is better able to grasp the opportunities provided by the growing wealth of digital information. Computing has, of course, already become a fundamental tool in all research disciplines. The UK e‐Science programme (2001–06)—since emulated internationally—pioneered the invention and use of new research methods, and a new wave of innovations in digital‐information technologies which have enabled them. The Strategy argues that the UK must now harness and leverage its own, plus the now global, investment in digital‐information technology in order to spread the benefits as widely as possible in research, education, industry and government. Implementing the Strategy would deliver the computational infrastructure and its benefits as envisaged in the Science & Innovation Investment Framework 2004–2014 (July 2004), and in the reports developing those proposals. To achieve this, the Strategy proposes the following actions: 1. support the continuous innovation of digital‐information research methods; 2. provide easily used, pervasive and sustained e‐Infrastructure for all research; 3. enlarge the productive research community which exploits the new methods efficiently; 4. generate capacity, propagate knowledge and develop skills via new curricula; and 5. develop coordination mechanisms to improve the opportunities for interdisciplinary research and to make digital‐infrastructure provision more cost effective. To gain the best value for money strategic coordination is required across a broad spectrum of stakeholders. A coherent strategy is essential in order to establish and sustain the UK as an international leader of well‐curated national data assets and computational infrastructure, which is expertly used to shape policy, support decisions, empower researchers and to roll out the results to the wider benefit of society. The value of data as a foundation for wellbeing and a sustainable society must be appreciated; national resources must be more wisely directed to the collection, curation, discovery, widening access, analysis and exploitation of these data. Every researcher must be able to draw on skills, tools and computational resources to develop insights, test hypotheses and translate inventions into productive use, or to extract knowledge in support of governmental decision making. This foundation plus the skills developed will launch significant advances in research, in business, in professional practice and in government with many consequent benefits for UK citizens. The Strategy presented here addresses these complex and interlocking requirements. VL - 27 ER - TY - JOUR T1 - Using the DCC Lifecycle Model to Curate a Gene Expression Database: A Case Study JF - International Journal of Digital Curation Y1 - 2009 A1 - O’Donoghue, J. A1 - van Hemert, J. I. AB - Developmental Gene Expression Map (DGEMap) is an EU-funded Design Study, which will accelerate an integrated European approach to gene expression in early human development. As part of this design study, we have had to address the challenges and issues raised by the long-term curation of such a resource. As this project is primarily one of data creators, learning about curation, we have been looking at some of the models and tools that are already available in the digital curation field in order to inform our thinking on how we should proceed with curating DGEMap. This has led us to uncover a wide range of resources for data creators and curators alike. Here we will discuss the future curation of DGEMap as a case study. We believe our experience could be instructive to other projects looking to improve the curation and management of their data. PB - UKOLN VL - 4 UR - http://www.ijdc.net/index.php/ijdc/article/view/134 IS - 3 ER - TY - JOUR T1 - A Grid infrastructure for parallel and interactive applications JF - Computing and Informatics Y1 - 2008 A1 - Gomes, J. A1 - Borges, B. A1 - Montecelo, M. A1 - David, M. A1 - Silva, B. A1 - Dias, N. A1 - Martins, JP A1 - Fernandez, C. A1 - Garcia-Tarres, L. , A1 - Veiga, C. A1 - Cordero, D. A1 - Lopez, J. A1 - J Marco A1 - Campos, I. A1 - Rodríguez, David A1 - Marco, R. A1 - Lopez, A. A1 - Orviz, P. A1 - Hammad, A. VL - 27 IS - 2 ER - TY - JOUR T1 - The interactive European Grid: Project objectives and achievements JF - Computing and Informatics Y1 - 2008 A1 - J Marco A1 - Campos, I. A1 - Coterillo, I. A1 - Diaz, I. A1 - Lopez, A. A1 - Marco, R. A1 - Martinez-Rivero, C. A1 - Orviz, P. A1 - Rodríguez, David A1 - Gomes, J. A1 - Borges, G. A1 - Montecelo, M. A1 - David, M. A1 - Silva, B. A1 - Dias, N. A1 - Martins, JP A1 - Fernandez, C. A1 - Garcia-Tarres, L. VL - 27 IS - 2 ER - TY - CONF T1 - Interaction as a Grounding for Peer to Peer Knowledge Sharing T2 - Advances in Web Semantics Y1 - 2007 A1 - Robertson, D. A1 - Walton, C. A1 - Barker, A. A1 - Besana, P. A1 - Chen-Burger, Y. A1 - Hassan, F. A1 - Lambert, D. A1 - Li, G. A1 - McGinnis, J A1 - Osman, N. A1 - Bundy, A. A1 - McNeill, F. A1 - van Harmelen, F. A1 - Sierra, C. A1 - Giunchiglia, F. JF - Advances in Web Semantics PB - LNCS-IFIP VL - 1 ER - TY - Generic T1 - Experience with the international testbed in the crossgrid project T2 - Advances in Grid Computing-EGC 2005 Y1 - 2005 A1 - Gomes, J. A1 - David, M. A1 - Martins, J. A1 - Bernardo, L. A1 - A García A1 - Hardt, M. A1 - Kornmayer, H. A1 - Marco, Jesus A1 - Marco, Rafael A1 - Rodríguez, David A1 - Diaz, Irma A1 - Cano, Daniel A1 - Salt, J. A1 - Gonzalez, S. A1 - J Sánchez A1 - Fassi, F. A1 - Lara, V. A1 - Nyczyk, P. A1 - Lason, P. A1 - Ozieblo, A. A1 - Wolniewicz, P. A1 - Bluj, M. A1 - K Nawrocki A1 - A Padee A1 - W Wislicki ED - Peter M. A. Sloot, Alfons G. Hoekstra, Thierry Priol, Alexander Reinefeld ED - Marian Bubak JF - Advances in Grid Computing-EGC 2005 T3 - LNCS PB - Springer Berlin/Heidelberg CY - Amsterdam VL - 3470 ER - TY - CONF T1 - Organization of the International Testbed of the CrossGrid Project T2 - Cracow Grid Workshop 2005 Y1 - 2005 A1 - Gomes, J. A1 - David, M. A1 - Martins, J. A1 - Bernardo, L. A1 - Garcia, A. A1 - Hardt, M. A1 - Kornmayer, H. A1 - Marco, Rafael A1 - Rodríguez, David A1 - Diaz, Irma A1 - Cano, Daniel A1 - Salt, J. A1 - Gonzalez, S. A1 - Sanchez, J. A1 - Fassi, F. A1 - Lara, V. A1 - Nyczyk, P. A1 - Lason, P. A1 - Ozieblo, A. A1 - Wolniewicz, P. A1 - Bluj, M. JF - Cracow Grid Workshop 2005 ER - TY - CHAP T1 - Persistence and Java — A Balancing Act T2 - Objects and Databases Y1 - 2001 A1 - Atkinson, M. ED - Klaus Dittrich ED - Giovanna Guerrini ED - Isabella Merlo ED - Marta Oliva ED - M. Elena Rodriguez AB - Large scale and long-lived application systems, enterprise applications, require persistence, that is provision of storage for many of their data structures. The JavaTM programming language is a typical example of a strongly-typed, object-oriented programming language that is becoming popular for building enterprise applications. It therefore needs persistence. The present options for obtaining this persistence are reviewed. We conclude that the Orthogonal Persistence Hypothesis, OPH, is still persuasive. It states that the universal and automated provision of longevity or brevity for all data will significantly enhance developer productivity and improve applications. This position paper reports on the PJama project with particular reference to its test of the OPH. We review why orthogonal persistence has not been taken up widely, and why the OPH is still incompletely tested. This leads to a more general challenge of how to conduct experiments which reveal large-scale and long-term effects and some thoughts on how that challenge might be addressed by the software research community. JF - Objects and Databases T3 - Lecture Notes in Computer Science PB - Springer VL - 1944 UR - http://www.springerlink.com/content/8t7x3m1ehtdqk4bm/?p=7ece1338fff3480b83520df395784cc6&pi=0 ER - TY - Generic T1 - VLDB'99, Proceedings of 25th International Conference on Very Large Data Bases, September 7-10, 1999, Edinburgh, Scotland, UK Y1 - 1999 A1 - Atkinson, Malcolm P. A1 - Maria E. Orlowska A1 - Patrick Valduriez A1 - Stanley B. Zdonik A1 - Michael L. Brodie ED - Atkinson, Malcolm P. ED - Maria E. Orlowska ED - Patrick Valduriez ED - Stanley B. Zdonik ED - Michael L. Brodie PB - Morgan Kaufmann SN - 1-55860-615-7 ER -