| 1. |
- Voitsekhovitch, I., et al.
(författare)
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Recent EUROfusion Achievements in Support of Computationally Demanding Multiscale Fusion Physics Simulations and Integrated Modeling
- 2018
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Ingår i: Fusion Science and Technology. - : Informa UK Limited. - 1536-1055 .- 1943-7641. ; 74:3, s. 186-197
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Tidskriftsartikel (refereegranskat)abstract
- © 2018, © 2018 The Authors. Published with license by Taylor & Francis Group, LLC. Integrated modeling (IM) of present experiments and future tokamak reactors requires the provision of computational resources and numerical tools capable of simulating multiscale spatial phenomena as well as fast transient events and relatively slow plasma evolution within a reasonably short computational time. Recent progress in the implementation of the new computational resources for fusion applications in Europe based on modern supercomputer technologies (supercomputer MARCONI-FUSION), in the optimization and speedup of the EU fusion-related first-principle codes, and in the development of a basis for physics codes/modules integration into a centrally maintained suite of IM tools achieved within the EUROfusion Consortium is presented. Physics phenomena that can now be reasonably modelled in various areas (core turbulence and magnetic reconnection, edge and scrape-off layer physics, radio-frequency heating and current drive, magnetohydrodynamic model, reflectometry simulations) following successful code optimizations and parallelization are briefly described. Development activities in support to IM are summarized. They include support to (1) the local deployment of the IM infrastructure and access to experimental data at various host sites, (2) the management of releases for sophisticated IM workflows involving a large number of components, and (3) the performance optimization of complex IM workflows.
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| 2. |
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| 3. |
- Strand, Pär, 1968, et al.
(författare)
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A European infrastructure for fusion simulations
- 2010
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Ingår i: Proceedings of the 18th Euromicro Conference on Parallel, Distributed and Network-Based Processing, PDP 2010. - 9780769539393 ; , s. 460-467
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The Integrated Tokamak Modelling Task Force (ITM-TF) is developing an infrastructure where the validation needs, as being formulated in terms of multi-device data access and detailed physics comparisons aiming for inclusion of synthetic diagnostics in the simulation chain, are key components. A device independent approach to data transport and a standardized approach to data management (data structures, naming, and access) is being developed in order to allow cross validation between different fusion devices using a single toolset. The effort is focused on ITER plasmas and ITER scenario development on current fusion device. The modeling tools are, however, aimed for general use and can be promoted in other areas of modelling as well. Extensive work has already gone into the development of standardized descriptions of the data (Consistent Physical Objects) providing initial steps towards a complete fusion modelling ontology. The longer term aim is a complete simulation platform which is expected to last and be extended in different ways for the coming 30 years. The technical underpinning is therefore of vital importance. In particular, the platform needs to be extensible and open-ended to be able to take full advantage of not only today's most advanced technologies but also be able to marshal future developments. A full level comprehensive prediction of ITER physics rapidly becomes expensive in terms of computing resources and may cover a range of computing paradigms. The simulation framework therefore needs to be able to use both grid and HPC computing facilities. Hence, data access and code coupling technologies are required to be available for a heterogeneous, possibly distributed, environment. The developments in this area are pursued in a separate project - EUFORIA (EU Fusion for ITER Applications). The current status of ITM-TF and EUFORIA is presented and discussed. © 2010 IEEE.
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| 4. |
- Frassinetti, Lorenzo, et al.
(författare)
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Pedestal structure, stability and scalings in JET-ILW : the EUROfusion JET-ILW pedestal database
- 2021
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 0029-5515 .- 1741-4326. ; 61:1
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Tidskriftsartikel (refereegranskat)abstract
- The EUROfusion JET-ILW pedestal database is described, with emphasis on three main issues. First, the technical aspects are introduced, including a description of the data selection, the datasets, the diagnostics used, the experimental and theoretical methods implemented and the main definitions. Second, the JET-ILW pedestal structure and stability are described. In particular, the work describes the links between the engineering parameters (power, gas and divertor configuration) and the disagreement with the peeling-ballooning (PB) model implemented with ideal magnetohydrodynamics equations. Specifically, the work clarifies why the JET-ILW pedestal tends to be far from the PB boundary at high gas and high power, showing that a universal threshold in power and gas cannot be found but that the relative shift (the distance between the position of the pedestal density and of the pedestal temperature) plays a key role. These links are then used to achieve an empirical explanation of the behavior of the JET-ILW pedestal pressure with gas, power and divertor configuration. Third, the pedestal database is used to revise the scaling law of the pedestal stored energy. The work shows a reasonable agreement with the earlier Cordey scaling in terms of plasma current and triangularity dependence, but highlights some differences in terms of power and isotope mass dependence.
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| 5. |
- Guillerminet, B., et al.
(författare)
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High Performance Computing tools for the Integrated Tokamak Modelling project
- 2010
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Ingår i: Fusion Engineering and Design. - : Elsevier BV. - 0920-3796. ; 85:3-4, s. 388 - 393
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Tidskriftsartikel (refereegranskat)abstract
- Fusion Modelling and Simulation are very challenging and the High Performance Computing issues are addressed here. Toolset for jobs launching and scheduling, data communication and visualization have been developed by the EUFORIA project and used with a plasma edge simulation code.
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| 6. |
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| 7. |
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| 8. |
- Imbeaux, F., et al.
(författare)
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Design and first applications of the ITER integrated modelling & analysis suite
- 2015
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 55:12
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Tidskriftsartikel (refereegranskat)abstract
- The ITER Integrated Modelling & Analysis Suite (IMAS) will support both plasma operation and research activities on the ITER tokamak experiment. The IMAS will be accessible to all ITER members as a key tool for the scientific exploitation of ITER. The backbone of the IMAS infrastructure is a standardized, machine-generic data model that represents simulated and experimental data with identical structures. The other outcomes of the IMAS design and prototyping phase are a set of tools to access data and design integrated modelling workflows, as well as first plasma simulators workflows and components implemented with various degrees of modularity.
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| 9. |
- Owsiak, M., et al.
(författare)
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Running simultaneous Kepler sessions for the parallelization of parametric scans and optimization studies applied to complex workflows
- 2016
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Ingår i: Procedia Computer Science. - : Elsevier. - 1877-0509. ; , s. 690-699
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Konferensbidrag (refereegranskat)abstract
- In this paper we present an approach taken to run multiple Kepler sessions at the same time. This kind of execution is one of the requirements for Integrated Tokamak Modelling platform developed by the Nuclear Fusion community within the context of EUROFusion project [2]. The platform is unique and original: it entails the development of a comprehensive and completely generic tokamak simulator including both the physics and the machine, which can be applied for any fusion device. All components are linked inside work ows. This approach allows complex coupling of various algorithms while at the same time provides consistency. Work ows are composed of Kepler and Ptolemy II elements as well as set of the native libraries written in various languages (Fortran, C, C++). In addition to that, there are Python based components that are used for visualization of results as well as for pre/post processing. At the bottom of all these components there is a database layer that may vary between software releases, and require di erent version of access libraries. The community is using shared virtual research environment to prepare and execute work ows. All these constraints make running multiple Kepler sessions really challenging. However, ability to run numerous sessions in parallel is a must - to reduce computation time and to make it possible to run released codes while working with new software at the same time. In this paper we present our approach to solve this issue and examples that show its correctness.
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| 10. |
- Plociennik, M., et al.
(författare)
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Application scenarios using serpens suite for Kepler scientific workflow system
- 2012
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Ingår i: Procedia Computer Science. - : Elsevier BV. - 1877-0509. ; 9, s. 1604-1613
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Konferensbidrag (refereegranskat)abstract
- This paper presents the overview of exploitation scenarios making use of the Serpens suite for the Kepler workflow orchestration system. The proposed framework provides researchers with an easy-to-use, workflow-based environment for scientific computations. It allows execution of various applications coming from different disciplines, in various distributed computational environments using a user-friendly interface. This research has been driven initially by Nuclear Fusion applications' requirements, where the leading idea was to enhance the modeling capabilities for ITER sized plasma research by providing access to High Performance Computing resources. Several usage scenarios are being presented with an example of applications from the field of Nuclear Fusion, Astrophysics and Computational Chemistry.
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| 11. |
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| 12. |
- Coster, D., et al.
(författare)
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Towards making fusion data FAIR
- 2021
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Ingår i: Proceedings - IEEE 17th International Conference on eScience, eScience 2021. ; , s. 233-234
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Konferensbidrag (refereegranskat)abstract
- The concept of FAIR data is being increasingly adopted at national and global levels as a way of maximising the impact and transparency of publicly-funded research outcomes and data. In this paper we introduce the FAIR requirements of the Fusion community as well as technological directions proposed by the Fair4Fusion project aiming at increasing the accessibility to fusion data.
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| 13. |
- Frassinetti, Lorenzo, et al.
(författare)
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The EUROfusion JET-ILW pedestal database
- 2018
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Ingår i: 45th EPS Conference on Plasma Physics, EPS 2018. - : European Physical Society (EPS). ; , s. 1056-1059
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Konferensbidrag (refereegranskat)
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| 14. |
- Frauel, Y., et al.
(författare)
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Easy use of high performance computers for fusion simulations
- 2012
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Ingår i: Fusion Engineering and Design. - : Elsevier BV. - 0920-3796. ; 87:12, s. 2057-2062
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Tidskriftsartikel (refereegranskat)abstract
- Fusion Modelling and Simulation are very challenging and the high performance computing issues are addressed here. Based on the framework developed by the European Integrated Tokamak Modelling project and on the EUFORIA infrastructure, a tool solving nicely these difficulties has been developed for the end users and applied to several fusion simulation cases. The first part recalls the issues with GRID and high performance computing, while the second part presents the solutions and the tool for developing easily a GRID/HPC actor. The last part reports the use of this tool in MHD equilibrium and plasma edge simulations.
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| 15. |
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| 16. |
- Kobiela, A, et al.
(författare)
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Exposure of Keratinocytes to Candida Albicans in the Context of Atopic Milieu Induces Changes in the Surface Glycosylation Pattern of Small Extracellular Vesicles to Enhance Their Propensity to Interact With Inhibitory Siglec Receptors
- 2022
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Ingår i: Frontiers in immunology. - : Frontiers Media SA. - 1664-3224. ; 13, s. 884530-
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Tidskriftsartikel (refereegranskat)abstract
- Candida albicans (C. albicans) infection is a potential complication in the individuals with atopic dermatitis (AD) and can affect clinical course of the disease. Here, using primary keratinocytes we determined that atopic milieu promotes changes in the interaction of small extracellular vesicles (sEVs) with dendritic cells and that this is further enhanced by the presence of C. albicans. sEV uptake is largely dependent on the expression of glycans on their surface; modelling of the protein interactions indicated that recognition of this pathogen through C. albicans-relevant pattern recognition receptors (PRRs) is linked to several glycosylation enzymes which may in turn affect the expression of sEV glycans. Here, significant changes in the surface glycosylation pattern, as determined by lectin array, could be observed in sEVs upon a combined exposure of keratinocytes to AD cytokines and C. albicans. This included enhanced expression of multiple types of glycans, for which several dendritic cell receptors could be proposed as binding partners. Blocking experiments showed predominant involvement of the inhibitory Siglec-7 and -9 receptors in the sEV-cell interaction and the engagement of sialic acid-containing carbohydrate moieties on the surface of sEVs. This pointed on ST6 β-Galactoside α-2,6-Sialyltransferase 1 (ST6GAL1) and Core 1 β,3-Galactosyltransferase 1 (C1GALT1) as potential enzymes involved in the process of remodelling of the sEV surface glycans upon C. albicans exposure. Our results suggest that, in combination with atopic dermatitis milieu, C. albicans promotes alterations in the glycosylation pattern of keratinocyte-derived sEVs to interact with inhibitory Siglecs on antigen presenting cells. Hence, a strategy aiming at this pathway to enhance antifungal responses and restrict pathogen spread could offer novel therapeutic options for skin candidiasis in AD.
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| 17. |
- Strand, Pär, 1968, et al.
(författare)
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A FAIR based approach to data sharing in Europe
- 2022
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Ingår i: Plasma Physics and Controlled Fusion. - : IOP Publishing. - 1361-6587 .- 0741-3335. ; 64:10
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Tidskriftsartikel (refereegranskat)abstract
- The European fusion research activities have, over recent decades, generated a vast and varied set of data. The volume and diversity of the data that need to be catalogued and annotated make the task of organising and making the data available within a broader environment very challenging. Nevertheless, there are strong scientific drivers as well as incentives and mandates from national research agencies suggesting that a more coherent approach to data referencing, dissemination and sharing would provide strong benefits to the fusion research community and beyond. Here, we discuss the technical requirements and developments needed to transition the current, and future, range of fusion research data to an open and Findable, Accessible, Interoperable, and Reusable data sharing structure guided by the principle 'as open as possible, as closed as necessary'. Here we propose a set of recommendations and technical implementations needed to form a European data sharing environment for the fusion research programmes. Consistency with the emerging IMAS (ITER Integrated Modelling and Analysis Suite) infrastructure is considered to facilitate future deployments.
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| 18. |
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| 19. |
- Falchetto, G. L., et al.
(författare)
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The European Integrated Tokamak Modelling (ITM) effort: achievements and first physics results
- 2014
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Ingår i: Nuclear Fusion. - : IOP Publishing. - 1741-4326 .- 0029-5515. ; 54:4
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Tidskriftsartikel (refereegranskat)abstract
- A selection of achievements and first physics results are presented of the European Integrated Tokamak Modelling Task Force (EFDA ITM-TF) simulation framework, which aims to provide a standardized platform and an integrated modelling suite of validated numerical codes for the simulation and prediction of a complete plasma discharge of an arbitrary tokamak. The framework developed by the ITM-TF, based on a generic data structure including both simulated and experimental data, allows for the development of sophisticated integrated simulations (workflows) for physics application.The equilibrium reconstruction and linear magnetohydrodynamic (MHD) stability simulation chain was applied, in particular, to the analysis of the edgeMHDstability of ASDEX Upgrade type-I ELMy H-mode discharges and ITER hybrid scenario, demonstrating the stabilizing effect of an increased Shafranov shift on edge modes. Interpretive simulations of a JET hybrid discharge were performed with two electromagnetic turbulence codes within ITM infrastructure showing the signature of trapped-electron assisted ITG turbulence. A successful benchmark among five EC beam/ray-tracing codes was performed in the ITM framework for an ITER inductive scenario for different launching conditions from the equatorial and upper launcher, showing good agreement of the computed absorbed power and driven current. Selected achievements and scientific workflow applications targeting key modelling topics and physics problems are also presented, showing the current status of the ITM-TF modelling suite.
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