| 1. |
- Konstantinov, A., et al.
(författare)
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Data management services of NorduGrid
- 2005
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Ingår i: CERN-2005-002. ; 2, s. 765-766
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Konferensbidrag (refereegranskat)abstract
- In common grid installations, services responsible for storing big data chunks, replication of those data and indexing their availability are usually completely decoupled. And a task of synchronizing data is passed to either user-level tools or separate services (like spiders) which are subject to failure and usually cannot perform properly if one of underlying services fails too. The NorduGrid Smart Storage Element (SSE) was designed to try to overcome those problems by combining the most desirable features into one service. It uses HTTPS/G for secure data transfer, Web Services for control (through same HTTPS/G channel) and can provide information to indexing services used in middlewares based on the Globus Toolkit (TM). At the moment, those are the Replica Catalog and the Replica Location Service. The modular internal design of the SSE and the power of C++ object programming allows to add support for other indexing services in an easy way. There are plans to complement it with a Smart Indexing Service capable of resolving inconsistencies hence creating a robust distributed data storage system.
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| 2. |
- Langgard Nielsen, J., et al.
(författare)
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Experiences with Data Indexing services supported by the NorduGrid middleware
- 2005
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Ingår i: CERN-2005-002. ; 2, s. 673-675
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Konferensbidrag (refereegranskat)abstract
- The NorduGrid middleware, ARC, has integrated support for querying and registering to Data Indexing services such as the Globus Replica Catalog and Globus Replica Location Server. This support allows one to use these indexing services for for example brokering during jobsubmission, automatic registration of files and many other things. This integrated support is complemented by a set of command-line tools for registering to and querying these Data Indexing services. In this article we will describe experiences with these indexing services both from a daily work point of view and in production environments such as the Atlas Data- Challenges 1 and 2. We will describe the advantages of such Data Indexing services as well as their shortcomings. Finally we will present a proposal for an extended Smart Indexing Service which should deal with the shortcomings described. Such an indexing service is being designed at the moment.
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| 3. |
- Pajchel, K., et al.
(författare)
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Usage statistics and usage patterns on the NorduGrid: Analyzing the logging information collected on one of the largest production Grids of the world
- 2005
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Ingår i: CERN-2005-002. ; 2, s. 711-714
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Konferensbidrag (refereegranskat)abstract
- The Nordic Grid facility (NorduGrid [1]) came into operation during summer 2002 when the Scandinavian ATLAS HEP group started to use the Grid for the ATLAS Data Challenges (DC) and was thus the first Grid ever contributing to an ATLAS production. Since then, the Grid facility has been in continuous 24/7 operation. NorduGrid is being used by a growing set of active users from various scientific areas including physics, chemistry, biology and informatics. It has given major contributions to the ATLAS Data Challenge 1 [2] and the ongoing Data Challenge 2. · The increasing number of resources has made NorduGrid one of the largest production Grids in the world, continuously running on more than 30 sites more than 3000 CPUs. · The resources range from small test clusters at academic institutions to large farms at several supercomputer centers and the NorduGrid software runs on clusters with very different Linux distributions. This presentation gives a short overview of the design and implementation of the NorduGrid middleware, logging and monitoring facilities. It will be followed by a description of a typical job on NorduGrid and the information about its parameters which are monitored online and persistified in the logging service.
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| 4. |
- Kevei, Eva, et al.
(författare)
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Forward genetic analysis of the circadian clock separates the multiple functions of ZEITLUPE.
- 2006
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Ingår i: Plant Physiology. - : Oxford University Press (OUP). - 0032-0889 .- 1532-2548. ; 140:3, s. 933-45
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Tidskriftsartikel (refereegranskat)abstract
- The circadian system of Arabidopsis (Arabidopsis thaliana) includes feedback loops of gene regulation that generate 24-h oscillations. Components of these loops remain to be identified; none of the known components is completely understood, including ZEITLUPE (ZTL), a gene implicated in regulated protein degradation. ztl mutations affect both circadian and developmental responses to red light, possibly through ZTL interaction with PHYTOCHROME B (PHYB). We conducted a large-scale genetic screen that identified additional clock-affecting loci. Other mutants recovered include 11 new ztl alleles encompassing mutations in each of the ZTL protein domains. Each mutation lengthened the circadian period, even in dark-grown seedlings entrained to temperature cycles. A mutation of the LIGHT, OXYGEN, VOLTAGE (LOV)/Period-ARNT-Sim (PAS) domain was unique in retaining wild-type responses to red light both for the circadian period and for control of hypocotyl elongation. This uncoupling of ztl phenotypes indicates that interactions of ZTL protein with multiple factors must be disrupted to generate the full ztl mutant phenotype. Protein interaction assays showed that the ztl mutant phenotypes were not fully explained by impaired interactions with previously described partner proteins Arabidopsis S-phase kinase-related protein 1, TIMING OF CAB EXPRESSION 1, and PHYB. Interaction with PHYB was unaffected by mutation of any ZTL domain. Mutation of the kelch repeat domain affected protein binding at both the LOV/PAS and the F-box domains, indicating that interaction among ZTL domains leads to the strong phenotypes of kelch mutations. Forward genetics continues to provide insight regarding both known and newly discovered components of the circadian system, although current approaches have saturated mutations at some loci.
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| 5. |
- Chaloupka, Milani, et al.
(författare)
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Encouraging outlook for recovery of a once severely exploited marine megaherbivore
- 2008
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-8238 .- 1466-822X. ; 17:2, s. 297-304
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Tidskriftsartikel (refereegranskat)abstract
- Aim To critically review the status of the green sea turtle (Chelonia mydas) using the best available scientific studies as there is a prevailing view that this species is globally endangered and its marine ecosystem functions compromised. Location Ogasawara (Japan), Hawaii (USA), Great Barrier Reef (Australia), Florida (USA), Tortuguero (Costa Rica). Methods We compiled seasonal nesting activity data from all reliable continuous long-term studies (> 25 years), which comprised data series for six of the world's major green turtle rookeries. We estimated the underlying time-specific trend in these six rookery-specific nester or nest abundance series using a generalized smoothing spline regression approach. Results Estimated rates of nesting population increase ranged from c. 4-14% per annum over the past two to three decades. These rates varied considerably among the rookeries, reflecting the level of historical exploitation. Similar increases in nesting population were also evident for many other green turtle stocks that have been monitored for shorter durations than the long-term studies presented here. Main conclusions We show that six of the major green turtle nesting populations in the world have been increasing over the past two to three decades following protection from human hazards such as exploitation of eggs and turtles. This population recovery or rebound capacity is encouraging and suggests that the green turtle is not on the brink of global extinction even though some stocks have been seriously depleted and are still below historical abundance levels. This demonstrates that relatively simple conservation strategies can have a profound effect on the recovery of once-depleted green turtle stocks and presumably the restoration of their ecological function as major marine consumers.
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| 6. |
- Ellert, Mattias, et al.
(författare)
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Advanced Resource Connector middleware for lightweight computational Grids
- 2007
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Ingår i: Future generations computer systems. - : Elsevier BV. - 0167-739X .- 1872-7115. ; 23:2, s. 219-240
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Tidskriftsartikel (refereegranskat)abstract
- As computational Grids move away from the prototyping state, reliability, performance and ease of use and maintenance become focus areas of their adoption. In this paper, we describe ARC (Advanced Resource Connector) Grid middleware, where these issues have been given special consideration. We present an in-depth view of the existing components of ARC, and discuss some of the new components, functionalities and enhancements currently under development. This paper also describes architectural and technical choices that have been made to ensure scalability, stability and high performance. The core components of ARC have already been thoroughly tested in demanding production environments, where it has been in use since 2002. The main goal of this paper is to provide a first comprehensive description of ARC.
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| 7. |
- Etz, Corina, et al.
(författare)
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Magnetic properties of FeCo nanoclusters on Cu(100 : Ab initio calculations
- 2007
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Ingår i: Physical Review B. Condensed Matter and Materials Physics. - 1098-0121 .- 1550-235X. ; 75:24
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Tidskriftsartikel (refereegranskat)abstract
- We present ab initio calculations of the magnetic moments and magnetic anisotropy energies of small FeCo clusters of varying composition on top of a Cu(100) substrate. Three different cluster layouts have been considered, namely, 2×2, 3×3, and crosslike pentamer clusters. The ratio of Co atoms with respect to the total number in a chosen cluster ("concentration") was varied and all possible arrangements of the atomic species were taken into account. Calculations have been performed fully relativistic using the embedded-cluster technique in conjunction with the screened Korringa-Kohn- Rostoker method and the magnetocrystalline anisotropy energy (MAE) has been evaluated by means of the magnetic force theorem. A central result of the investigations is that the size of the magnetic moments of the individual Fe and Co atoms and their contributions to the anisotropy energy depend on the position they occupy in a particular cluster and on the type and the number of nearest neighbors. The MAE for the 2×2 and 3×3 clusters varies with respect to the concentration of Co atoms in the same manner as the corresponding monolayer case, whereas the pentamer clusters show a slightly different behavior. Furthermore, for the clusters with an easy axis along a direction in the surface plane, the MAE shows a significant angular dependence.
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| 8. |
- Peni, T., et al.
(författare)
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Induced L2 norm improvement by interpolating controllers for discrete time LPV systems
- 2009
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Ingår i: European Journal of Control. - 0947-3580. ; 15:5, s. 1-15
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Tidskriftsartikel (refereegranskat)abstract
- The paper shows an interpolation-based control solution asapossible technique to formulate the constrained H∞ control problem for discrete-time linear parameter varying (LPV) systems. The control policy is constructed by interpolating amongapriori designed, unconstrained, constant, state feedback controllers. Invariant set theory is used to introduce the measure of the domain of applicability. It is shown that the `trade-off' between the performance and the size of the domain of applicability can be significantly reduced by controller interpolation. Hence, the interpolation-based controller becomes applicable overamuch larger region than any other single state feedback. The proposed method gives stabilizing solution not only under hard constraints, but also allows the online modification of the induced L² norm from the generalized disturbance input to the predefined performance output. Moreover, the suggested method can be applied in real-time environment.
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| 9. |
- Sturrock, R., et al.
(författare)
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Performance of the NorduGrid ARC and the Dulcinea Executor in ATLAS Data Challenge 2
- 2005
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Ingår i: CERN-2005-002. ; 2, s. 1095-1098
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Konferensbidrag (refereegranskat)abstract
- This talk describes the various stages of ATLAS Data Challenge 2 (DC2) in what concerns usage of resources deployed via NorduGrid's Advanced Resource Connector (ARC). It also describes the integration of these resources with the ATLAS production system using the Dulcinea executor. ATLAS Data Challenge 2 (DC2), run in 2004, was designed to be a step forward in the distributed data processing. In particular, much coordination of task assignment to resources was planned to be delegated to Grid in its different flavours. An automatic production management system was designed, to direct the tasks to Grids and conventional resources. The Dulcinea executor is a part of this system that provides interface to the information system and resource brokering capabilities of the ARC middleware. The executor translates the job definitions recieved from the supervisor to the extended resource specification language (XRSL) used by the ARC middleware. It also takes advantage of the ARC middleware's built-in support for the Globus Replica Location Server (RLS) for file registration and lookup. NorduGrid's ARC has been deployed on many ATLAS-dedicated resources across the world in order to enable effective participation in ATLAS DC2. This was the first attempt to harness large amounts of strongly heterogeneous resources in various countries for a single collaborative exercise using Grid tools. This talk addresses various issues that arose during different stages of DC2 in this environment: preparation, such as ATLAS software installation; deployment of the middleware; and processing. The results and lessons are summarized as well.
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| 10. |
- Székely, Anna J., et al.
(författare)
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DGGE and T-RFLP analysis of bacterial succession during mushroom compost production and sequence-aided T-RFLP profile of mature compost
- 2009
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Ingår i: Microbial Ecology. - : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 57:3, s. 522-533
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Tidskriftsartikel (refereegranskat)abstract
- The amount of button mushroom (Agaricus bisporus) harvested from compost is largely affected by the microbial processes taking place during composting and the microbes inhabiting the mature compost. In this study, the microbial changes during the stages of this specific composting process were monitored, and the dominant bacteria of the mature compost were identified to reveal the microbiological background of the favorable properties of the heat-treated phase II mushroom compost. 16S ribosomal deoxyribonucleic acid (rDNA)-based denaturing gradient gel electrophoresis (DGGE) and terminal restriction fragment length polymorphism (T-RFLP) molecular fingerprinting methods were used to track the succession of microbial communities in summer and winter composting cycles. DNA from individual DGGE bands were reamplified and subjected to sequence analysis. Principal component analysis of fingerprints of the composting processes showed intensive changes in bacterial community during the 22-day procedure. Peak temperature samples grouped together and were dominated by Thermus thermophilus. Mature compost patterns were almost identical by both methods (DGGE, T-RFLP). To get an in-depth analysis of the mature compost bacterial community, the sequence data from cultivation of the bacteria and cloning of environmental 16S rDNA were uniquely coupled with the output of the environmental T-RFLP fingerprints (sequence-aided T-RFLP). This method revealed the dominance of a supposedly cellulose-degrading consortium composed of phylotypes related to Pseudoxanthomonas, Thermobifida, and Thermomonospora. © 2008 Springer Science+Business Media, LLC.
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