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  • 51.
    Jansson, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). Basque Center for Applied Mathematics, Spain.
    Nava, V.
    Sanchez, M.
    Aguirre, G.
    De Abreu, Rodrigo Vilela
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). Basque Center for Applied Mathematics, Spain.
    Villate, J. L.
    Adaptive simulation of unsteady flow past the submerged part of a floating wind turbine platform2015Ingår i: MARINE 2015 - Computational Methods in Marine Engineering VI, International Center for Numerical Methods in Engineering (CIMNE), 2015, s. 35-46Konferensbidrag (Refereegranskat)
    Abstract [en]

    Offshore floating platforms for wind turbines represent challenging concepts for designers trying to combine an optimal compromise between cost effectiveness and performance. Modelling of the hydrodynamic behaviour of the structure is still the subject of wide debate in the technical communities. The assessment of the hydrodynamics of the support structure is not an easy task as the floaters consist of an assembly of columns, braces and pontoons, commonly also with heave plates: Each of these components corresponds to a different hydrodynamic model and it further interacts with the other elements. This results in very complex non-linear modeling, which makes it necessary to resort to computational fluid dynamics (CFD) methods for the evaluation of the combined hydrodynamics. In the framework of the collaboration between the Basque Centre for Applied Mathematics (BCAM) and Tecnalia R&I, the interaction of the sea flow with a semisubmersible floating offshore wind platform have been calculated by using the open source solver Unicorn in the FEniCS-HPC framework when subject to a steady inflow. The prototype of the platform consists in a semi-submersible 4-columns column stabilized platform - NAUTILUS Floating Solutions concept-; columns are connected by a rigid ring pontoon provided with heave damping plates at the bottom. The novelty of the approach in FEniCS-HPC hinges upon an implicit formulation for the turbulence, a cheap free slip model of the boundary layer and goal-oriented mesh adaptivity [8, 6, 9, 20, 1]. We find that the results are consistent with experimental results for cylinders at high Reynolds number.

  • 52.
    Jansson, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Basque Center for Applied Mathematics, Bilbao, Spain.
    Nguyen, Dang
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Margarida, Moragues
    BCAM - Basque Center for Applied Mathematics.
    Castanon, Daniel
    BCAM - Basque Center for Applied Mathematics.
    Saavedra, Laura
    Universidad Politécnica de Madrid.
    Krishnasamy, Ezhilmathi
    BCAM - Basque Center for Applied Mathematics.
    Goude, Anders
    Uppsala University.
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST). Basque Center for Applied Mathematics, Bilbao, Spain.
    Direct finite element simulation of turbulent flow for marine based renewable energyManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    In this article we present a computational framework for simulation ofturbulent flow in marine based renewable energy applications. Inparticular, we focus on floating structures and rotatingturbines. This work is an extension to multiphase turbulent flow, ofour existing framework of residual based turbulence modeling forsingle phase turbulent incompressible flow. We illustrate theframework in four examples: a regular wave test where we compareagainst an exact solution, the standard MARIN wave impact benchmarkwith experimental validation data, a vertical axis turbine withcomplex geometry from an existing turbine, and finally a prototypesimulation of decay test in a coupled moving boundary rigid-body andtwo-phase fluid simulation.

  • 53.
    Jansson, Johan
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Spühler, Jeannette
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Degirmenci, Cem
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Automated error control in finite element methods withapplications in fluid flow2014Rapport (Övrigt vetenskapligt)
    Abstract [en]

    In this paper we present a new adaptive finite element method for thesolution of linear and non-linear partial differential equationsdirectly using the a posteriori error representation as a local errorindicator, with the primal and dual solutions approximated in the samefinite element space, here piecewise continuous linear functions onthe same mesh. Since this approach gives a global a posteriori errorrepresentation that is zero due to Galerkin orthogonality, the errorrepresentation has traditionally been thought to contain noinformation about the error. However, for elliptic andconvection-diffusion model problems we show the opposite, that locallythe orthogonal error representation behaves very similar to thenon-orthogonal error representation using a higher order approximationof the dual.  We have previously proved an a priori estimate of thelocal error indicator for elliptic problems, and in this paper weextend the proof to convection-reaction problems. We also present aversion of the method for non-elliptic and non-linear problems using astabilized finite element method where the a posteriori errorrepresentation is no longer orthogonal. We apply this method to thestationary incompressible Navier-Stokes equation and perform detailednumerical experiments which show that the a posteriori error estimateis within a factor 2 of the error based on a reference value on a finemesh, except in a few data points on very coarse meshes for anon-smooth test case where it is within a factor 3.

  • 54.
    Jansson, Niclas
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    High Performance Adaptive Finite Element Methods: With Applications in Aerodynamics2013Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
    Abstract [sv]

    Den höga beräkningskostnaden för att lösa upp alla turbulenta skalor för ett realistiskt problem gör en direkt numerisk simulering av Navier-Stokes ekvationer omöjlig. De senaste framstegen inom adaptiva finita element metoder ger ett nytt kraftfullt verktyg inom Computational Fluid Dynamics (CFD). Beräkningskostnaden för en simulering av turbulent flöde kan minimeras genom att beräkningsnätet adaptivt förfinas baserat på en a posteriori feluppskattning. Dessa adaptiva metoder har tidigare implementerats för seriella beräkningar, medan en effektiv parallellisering av metoden inte är trivial. I denna avhandling presenterar vi vår utveckling av en adaptiv finita element lösare, anpassad för att effektivt beräkna tidsupplösta approximationer i komplicerade geometrier med a posteriori felkontroll. Effektiva datastrukturer och metoder för ostrukturerade beräkningsnät av tetrahedrar presenteras. Avhandlingen behandlar även effektiv parallellisering av lokala nätförfiningsmetoder, exempelvis recursive longest edge bisection. Även lastbalanseringsproblematiken behandlas, där problemet lösts genom utvecklandet av en prediktiv dynamisk lastbalanseringsmetod, baserad på en viktad dualgraf av beräkningsnätet. Slutligen avhandlas även problematiken med att effektivt utnyttja nytillkomna superdatorarkitekturer, genom utvecklandet av en hybrid parallelliserings modell som kombinerar traditionell meddelande baserad parallellisering med envägskommunikation. Detta har resulterat i en generell samt effektiv implementation med god skalning upp till fler än tolv tusen processorkärnor.

  • 55.
    Jansson, Niclas
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Optimizing Sparse Matrix Assembly in Finite Element Solvers with One-Sided Communication2013Ingår i: High Performance Computing for Computational Science - VECPAR 2012, Springer Berlin/Heidelberg, 2013, s. 128-139Konferensbidrag (Refereegranskat)
    Abstract [en]

    In parallel finite element solvers, sparse matrix assembly is often a bottleneck. Implemented using message passing, latency from message matching starts to limit performance as the number of cores increases. We here address this issue by using our own stack based representation of the sparse matrix, and a hybrid parallel programming model combining traditional message passing with one-sided communication. This gives an significantly faster insertion rate compared to state of the art implementations on a Cray XE6.

  • 56.
    Jansson, Niclas
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Towards a Parallel Algebraic Multigrid Solver Using Partitioned Global Address Space2013Rapport (Övrigt vetenskapligt)
    Abstract [en]

    The Algebraic Multigrid (AMG) method has over the years developed into an ecient tool for solving unstructured linear systems. The need to solve large industrial problems discretized on unstructured meshes, has been a key motivation for devising a parallel AMG method. Despite some success, the key part of the AMG algorithm; the coarsening step, is far from trivial to parallelize eciently. We here introduce a novel parallelization of the Ruge-Stüben coarsening algorithm, that retains the good interpolation properties of the original method. Our parallelization is based on the Partitioned Global Address Space (PGAS) abstraction, which allows for a simple, yet efficient implementation. The solver is described in detail and a performance study on a Cray XE6 is presented.

  • 57.
    Jansson, Niclas
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Improving Parallel Performance of FEniCS Finite Element Computations by Hybrid MPI/PGASManuskript (preprint) (Övrigt vetenskapligt)
    Abstract [en]

    We present our work on developing a hybrid parallel programming model for a general finite element solver. The main focus of our work is to demonstrate that legacy codes with high latency, two-sided communication in the form of message passing can be improved using lightweight one-sided communication. We introduce a new hybrid MPI/PGAS implementation of the open source general finite element framework FEniCS, replacing the linear algebra backend (PETSc) with a new library written in UPC. A detailed description of the linear algebra backend implementation and the hybrid interface to FEniCS is given. We also present a detailed analysis of the performance of this hybrid solver on the Cray XE6 Lindgren at PDC/KTH including a comparison with the MPI only implementation, where we find that the hybrid implementation results in significant improvements in performance of the solver.

  • 58.
    Jansson, Niclas
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Improving Parallel Performance of FEniCS Finite Element Computations by Hybrid MPI/PGAS2013Rapport (Övrigt vetenskapligt)
    Abstract [en]

    We present our work on developing a hybrid parallel programming model for a general finite element solver. The main focus of our work is to demonstrate that legacy codes with high latency, two-sided communication in the form of message passing can be improved using lightweight one-sided communication. We introduce a new hybrid MPI/PGAS implementation of the open source general finite element framework FEniCS, replacing the linear algebra backend (PETSc) with a new library written in UPC. A detailed description of the linear algebra backend implementation and the hybrid interface to FEniCS is given. We also present a detailed analysis of the performance of this hybrid solver on the Cray XE6 Lindgren at PDC/KTH including a comparison with the MPI only implementation, where we find that the hybrid implementation results in significant improvements in performance of the solver.

  • 59. Karagiannis, F.
    et al.
    Keramida, D.
    Ioannidis, Y.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Vitlacil, Dejan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Short, Faith
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Technological and organisational aspects of global research data infrastructures towards year 20202013Ingår i: Data Science Journal, ISSN 1683-1470, E-ISSN 1683-1470, Vol. 12, s. GRDI1-GRDI5Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A general-purpose Global Research Data Infrastructure (GRDI) for all sciences and research purposes is not conceivable for the next decade as there are too many discipline-specific modalities that currently prevail for such generalisation efforts to be effective. On the other hand, a more pragmatic approach is to start from what currently exists, identify best practices and key issues, and promote effective inter-domain collaboration among different components forming an ecosystem. This will promote interoperability, data exchange, data preservation, and distributed access (among others). This ecosystem of interoperable research data infrastructures will be composed of regional, disciplinary, and multidisciplinary components, such as libraries, archives, and data centres, offering data services for both primary datasets and publications. The ecosystem will support data-intensive science and research and stimulate the interaction among all its elements, thus promoting multidisciplinary and interdisciplinary science. This special issue includes a set of independent papers from renowned experts on organisational and technological issues related to GRDIs. These documents feed into and compliment the GRDI2020 roadmap, which supports a Global Research Data Infrastructure ecosystem.

  • 60. Karlsson, A.
    et al.
    Olofsson, N.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Clements, M.
    A parallel microsimulation package for modelling cancer screening policies2017Ingår i: Proceedings of the 2016 IEEE 12th International Conference on e-Science, e-Science 2016, IEEE, 2017, s. 323-330Konferensbidrag (Refereegranskat)
    Abstract [en]

    Microsimulation with stochastic life histories is an important tool in the development of public policies. In this article, we use microsimulation to evaluate policies for prostate cancer testing. We implemented the microsimulations as an R package, with pre- and post-processing in R and with the simulations written in C++. Calibrating a microsimulation model with a large population can be computationally expensive. To address this issue, we investigated four forms of parallelism: (i) shared memory parallelism using R; (ii) shared memory parallelism using OpenMP at the C++ level; (iii) distributed memory parallelism using R; and (iv) a hybrid shared/distributed memory parallelism using OpenMP at the C++ level and MPI at the R level. The close coupling between R and C++ offered advantages for ease of software dissemination and the use of high-level R parallelisation methods. However, this combination brought challenges when trying to use shared memory parallelism at the C++ level: the performance gained by hybrid OpenMP/MPI came at the cost of significant re-factoring of the existing code. As a case study, we implemented a prostate cancer model in the microsimulation package. We used this model to investigate whether prostate cancer testing with specific re-testing protocols would reduce harms and maintain any mortality benefit from prostate-specific antigen testing. We showed that four-yearly testing would have a comparable effectiveness and a marked decrease in costs compared with two-yearly testing and current testing. In summary, we developed a microsimulation package in R and assessed the cost-effectiveness of prostate cancer testing. We were able to scale up the microsimulations using a combination of R and C++, however care was required when using shared memory parallelism at the C++ level.

  • 61. Korovinskiy, D. B.
    et al.
    Divin, A. V.
    Erkaev, N. V.
    Semenov, V. S.
    Artemyev, A. V.
    Ivanova, V. V.
    Ivanov, I. B.
    Lapenta, G.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Biernat, H. K.
    The double-gradient magnetic instability: Stabilizing effect of the guide field2015Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 22, nr 1, artikel-id 012904Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The role of the dawn-dusk magnetic field component in stabilizing of the magnetotail flapping oscillations is investigated in the double-gradient model framework (Erkaev et al., Phys. Rev. Lett. 99, 235003 (2007)), extended for the magnetotail-like configurations with non-zero guide field By. Contribution of the guide field is examined both analytically and by means of linearized 2-dimensional (2D) and non-linear 3-dimensional (3D) MHD modeling. All three approaches demonstrate the same properties of the instability: stabilization of current sheet oscillations for short wavelength modes, appearing of the typical (fastest growing) wavelength lambda(peak) of the order of the current sheet width, decrease of the peak growth rate with increasing B-y value, and total decay of the mode for B-y similar to 0: 5 in the lobe magnetic field units. Analytical solution and 2D numerical simulations claim also the shift of lambda(peak) toward the longer wavelengths with increasing guide field. This result is barely visible in 3D simulations. It may be accounted for the specific background magnetic configuration, the pattern of tail-like equilibrium provided by approximated solution of the conventional Grad-Shafranov equation. The configuration demonstrates drastically changing radius of curvature of magnetic field lines, R-c. This, in turn, favors the "double-gradient" mode (lambda > R-c) in one part of the sheet and classical "ballooning" instability (lambda < R-c) in another part, which may result in generation of a "combined" unstable mode. (C) 2015 AIP Publishing LLC.

  • 62. Kumar, P.
    et al.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Lapenta, G.
    Meerbergen, K.
    Roose, D.
    High performance solvers for implicit particle in cell simulation2013Ingår i: 2013 International Conference on Computational Science, Elsevier, 2013, s. 2251-2258Konferensbidrag (Refereegranskat)
    Abstract [en]

    A three-dimensional implicit particle-in-cell (iPIC3D) method implemented by S. Markidis et. al. in ["Multiscale simulations of plasma with iPIC3D", Mathematics and Computers in Simulation, 80(2010), 1509-1519] allows time steps at magnetohydrodynamics time scale. The code requires the solution of two linear systems: A Poisson system related to divergence cleaning, and a system related to a second order formulation of Maxwell equation. In iPIC3D, the former is the most costly. To reduce the cost of solving the Poisson system, a parallel matrix assembly and partitioning method are implemented, and conjugate gradient and algebraic multigrid (AMG) solvers from the Hypre library are called. The scalability of AMG as a solver is studied for 1D and 3D partitionings and compared to that of CG.

  • 63. Lakatos, D.
    et al.
    Blackshaw, M.
    Olwal, Alex
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). GoogleMountain View, United States .
    Barryte, Z.
    Perlin, K.
    Ishii, H.
    T(ether): Spatially-aware handhelds, gestures and proprioception for multi-user 3D modeling and animation2014Ingår i: SUI 2014 - Proceedings of the 2nd ACM Symposium on Spatial User Interaction, Association for Computing Machinery (ACM), 2014, s. 90-93Konferensbidrag (Refereegranskat)
    Abstract [en]

    T(ether) is a spatially-aware display system for multi-user, collaborative manipulation and animation of virtual 3D objects. The handheld display acts as a window into virtual reality, providing users with a perspective view of 3D data. T(ether) tracks users' heads, hands, fingers and pinching, in addition to a handheld touch screen, to enable rich interaction with the virtual scene. We introduce gestural interaction techniques that exploit proprioception to adapt the UI based on the hand's position above, behind or on the surface of the display. These spatial interactions use a tangible frame of reference to help users manipulate and animate the model in addition to controlling environment properties. We report on initial user observations from an experiment for 3D modeling, which indicate T(ether)'s potential for embodied viewport control and 3D modeling interactions.

  • 64. Lapenta, Giovanni
    et al.
    Goldman, Martin
    Newman, David
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Propagation speed of rotation signals for field lines undergoing magnetic reconnection2013Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 20, nr 10, s. 102113-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Reconnection is associated with two bending of the magnetic field lines. Considering the usual plane of a 2D reconnection simulation, the first bending is in-plane and produces the needed topological changes by bringing oppositely directed filed lines in proximity. The second is typical of fast reconnection and is out of plane, leading to the formation of the Hall magnetic field. This second rotation has recently been observed to proceed at superAlfvenic speeds and to carry substantial energy fluxes (Shay et al., Phys. Rev. Lett. 107, 065001 (2011)). We revisit these rotations with a new diagnostics based on dispersing a multitude of virtual probes into a kinetic simulation, akin the approach of multi spacecraft missions. The results of the new diagnostics are compared with the theory of characteristics applied to the two fluid model. The comparison of virtual probes and the method of characteristics confirm the findings relative to the out of plane rotation and uncover the existence of two families of characteristics. Both are observed in the simulation. The early stage of reconnection develops on the slower compressional branch and the later faster phase develops on the faster torsional branch. The superAlfvenic signal is only relevant in the second phase.

  • 65. Lapenta, Giovanni
    et al.
    Goldman, Martin
    Newman, David
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Divin, Andrey
    Electromagnetic energy conversion in downstream fronts from three dimensional kinetic reconnection2014Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 21, nr 5, s. 055702-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The electromagnetic energy equation is analyzed term by term in a 3D simulation of kinetic reconnection previously reported by Vapirev et al. [J. Geophys. Res.: Space Phys. 118, 1435 (2013)]. The evolution presents the usual 2D-like topological structures caused by an initial perturbation independent of the third dimension. However, downstream of the reconnection site, where the jetting plasma encounters the yet unperturbed pre-existing plasma, a downstream front is formed and made unstable by the strong density gradient and the unfavorable local acceleration field. The energy exchange between plasma and fields is most intense at the instability, reaching several pW/m(3), alternating between load (energy going from fields to particles) and generator (energy going from particles to fields) regions. Energy exchange is instead purely that of a load at the reconnection site itself in a region focused around the x-line and elongated along the separatrix surfaces. Poynting fluxes are generated at all energy exchange regions and travel away from the reconnection site transporting an energy signal of the order of about S approximate to 10(-3)W/m(2). (C) 2014 AIP Publishing LLC.

  • 66. Lapenta, Giovanni
    et al.
    Goldman, Martin V.
    Newman, David L.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Energy exchanges in reconnection outflows2017Ingår i: Plasma Physics and Controlled Fusion, ISSN 0741-3335, E-ISSN 1361-6587, Vol. 59, nr 1, artikel-id 014019Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Reconnection outflows are highly energetic directed flows that interact with the ambient plasma or with flows from other reconnection regions. Under these conditions the flow becomes highly unstable and chaotic, as any flow jets interacting with a medium. We report here massively parallel simulations of the two cases of interaction between outflow jets and between a single outflow with an ambient plasma. We find in both case the development of a chaotic magnetic field, subject to secondary reconnection events that further complicate the topology of the field lines. The focus of the present analysis is on the energy balance. We compute each energy channel (electromagnetic, bulk, thermal, for each species) and find where the most energy is exchanged and in what form. The main finding is that the largest energy exchange is not at the reconnection site proper but in the regions where the outflowing jets are destabilized.

  • 67. Lapenta, Giovanni
    et al.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Divin, Andrey
    Newman, David
    Goldman, Martin
    Separatrices: The crux of reconnection2015Ingår i: Journal of Plasma Physics, ISSN 0022-3778, E-ISSN 1469-7807, Vol. 81, nr 1, artikel-id 325810109Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Magnetic reconnection is one of the key processes in astrophysical and laboratory plasmas: it is the opposite of a dynamo. Looking at energy, a dynamo transforms kinetic energy in magnetic energy while reconnection takes magnetic energy and returns it to its kinetic form. Most plasma processes at their core involve first storing magnetic energy accumulated over time and then releasing it suddenly. We focus here on this release. A key concept in analysing reconnection is that of the separatrix, a surface (line in 2D) that separates the fresh unperturbed plasma embedded in magnetic field lines not yet reconnected with the hotter exhaust embedded in reconnected field lines. In kinetic physics, the separatrices become a layer where many key processes develop. We present here new results relative to the processes at the separatrices that regulate the plasma flow, the energization of the species, the electromagnetic fields and the instabilities developing at the separatrices.

  • 68. Lapenta, Giovanni
    et al.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Goldman, Martin V.
    Newman, David L.
    Secondary reconnection sites in reconnection-generated flux ropes and reconnection fronts2015Ingår i: Nature Physics, ISSN 1745-2473, E-ISSN 1745-2481, Vol. 11, nr 8, s. 690-+Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The primary target of the Magnetospheric MultiScale (MMS) mission is the electron-scale diffusion layer around reconnection sites. Here we study where these regions are found in full three-dimensional simulations. In two dimensions the sites of electron diffusion, defined as the regions where magnetic topology changes and electrons move with respect to the magnetic field lines, are located near the reconnection site. But in three dimensions we find that the reconnection exhaust far from the primary reconnection site also becomes host to secondary reconnection sites. Four diagnostics are used to demonstrate the point: the direct observation of topology impossible without secondary reconnection, the direct measurement of topological field line breakage, the measurement of electron jets emerging from secondary reconnection regions, and the violation of the frozen-in condition. We conclude that secondary reconnection occurs in a large part of the exhaust, providing many more chances for MMS to find itself in the right region to hit its target.

  • 69. Lapenta, Giovanni
    et al.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Poedts, Stefaan
    Vucinic, Dean
    Space Weather Prediction and Exascale Computing2013Ingår i: Computing in science & engineering (Print), ISSN 1521-9615, E-ISSN 1558-366X, Vol. 15, nr 5, s. 68-76Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Space weather can have a great effect on Earth's climate. Predicting the impact of space environment disturbances on Earth presents a challenge to scientists. Here, the ExaScience Lab's efforts are presented, which use exascale computing and new visualization tools to predict the arrival and impact of space events on Earth.

  • 70. Lapenta, Giovanni
    et al.
    Pierrard, Viviane
    Keppens, Rony
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Poedts, Stefaan
    Sebek, Ondrej
    Travnicek, Pavel M.
    Henri, Pierre
    Califano, Francesco
    Pegoraro, Francesco
    Faganello, Matteo
    Olshevsky, Vyacheslav
    Restante, Anna Lisa
    Nordlund, Åke
    Frederiksen, Jacob Trier
    Mackay, Duncan H.
    Parnell, Clare E.
    Bemporad, Alessandro
    Susino, Roberto
    Borremans, Kris
    SWIFF: Space weather integrated forecasting framework2013Ingår i: Journal of Space Weather and Space Climate, ISSN 2115-7251, E-ISSN 2115-7251, Vol. 3, s. A05-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    SWIFF is a project funded by the Seventh Framework Programme of the European Commission to study the mathematical-physics models that form the basis for space weather forecasting. The phenomena of space weather span a tremendous scale of densities and temperature with scales ranging 10 orders of magnitude in space and time. Additionally even in local regions there are concurrent processes developing at the electron, ion and global scales strongly interacting with each other. The fundamental challenge in modelling space weather is the need to address multiple physics and multiple scales. Here we present our approach to take existing expertise in fluid and kinetic models to produce an integrated mathematical approach and software infrastructure that allows fluid and kinetic processes to be modelled together. SWIFF aims also at using this new infrastructure to model specific coupled processes at the Solar Corona, in the interplanetary space and in the interaction at the Earth magnetosphere.

  • 71.
    Larsson, David
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Spuhler, Jeannette H.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Nordenfur, Tim
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Colarieti-Tosti, Massimiliano
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Gao, Hang
    Larsson, Matilda
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Patient-specific flow simulation of the left ventricle from 4D echocardiography - feasibility and robustness evaluation2015Ingår i: 2015 IEEE INTERNATIONAL ULTRASONICS SYMPOSIUM (IUS), IEEE , 2015Konferensbidrag (Refereegranskat)
    Abstract [en]

    In recent years, computational fluid dynamics (CFD) simulations on in-silico models of the heart have provided a valuable insight into cardiac hemodynamic behaviour. However, so far most models have been either based on simplified geometries or on imaging acquisitions with relatively low temporal resolution. It has been suggested that models based entirely on subject-specific ultrasonic images should be used to capture transient flow changes. Therefore, the aim of this study is to present a pathway from routine 4D echocardiography to a patient-specific flow simulation of the left ventricle (LV), evaluating the model robustness and clinical feasibility. The created pathway consisted of initial LV segmentation and mitral/aortic valve positioning, being subsequently used as input for the CFD simulations (based on solving the Navier-Stokes equation using an Arbitrary Lagrangian-Eulerian approach). The output consisted of 4D blood flow velocities and relative pressures in the entire LV. On five subjects, the model robustness was evaluated with regards to variations in singular boundary conditions. The clinical feasibility of the output was compared to clinical PW Doppler measurements and, as a proof-of-concept, synthetic contrast enhanced ultrasound images were simulated on the flow field using the COLE-method. Results indicated a relatively robust model, with variations in regional flow of approximately 5.1/6.2% and 9.7/7.0% for healthy and pathological subject respectively (end diastole/end systole). Furthermore, showing similar behaviour to clinical Doppler measurements the technique serves as a promising tool for future clinical investigations. Additionally, the ability of simulating synthetic ultrasound images further underlines the applicability of the pathway, being potentially useful in studies on improved echocardiographic image analysis.

  • 72.
    Larsson, David
    et al.
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Spuhler, Jeannette H.
    Petersson, Sven
    Nordenfur, Tim
    Hoffman, Johan
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Colarieti-Tosti, Massimiliano
    Winter, Reidar
    Larsson, Matilda
    KTH, Skolan för teknik och hälsa (STH), Medicinsk teknik, Medicinsk bildteknik.
    Multimodal validation of patient-specific intraventricular flow simulations from 4D echocardiography2016Ingår i: 2016 IEEE INTERNATIONAL ULTRASONICS SYMPOSIUM (IUS), IEEE conference proceedings, 2016Konferensbidrag (Refereegranskat)
    Abstract [en]

    The combination of refined medical imaging techniques and computational fluid dynamics (CFD) models has enabled the study of complex flow behavior on a highly regional level. Recently, we have developed a platform for patient-specific CFD modelling of blood flow in the left ventricle (LV), with input data and required boundary conditions acquired from 4D echocardiography. The platform robustness has been evaluated with respect to input variable variations, but for any clinical implementation model flow validation is essential. Therefore, the aim of this study is to evaluate the accuracy of the patient-specific CFD model against multimodal image-based flow measurements. For the validation, 4D echocardiography was acquired from two healthy subjects, from which LV velocity fields were simulated. In-vivo flows from the same two subjects were then acquired by pulsed wave (PW) Doppler imaging over both LV-valves, and by cine phase-contract magnetic resonance imaging (PC-MRI) at eight defined anatomical planes in the LV. By fusing PC-MRI and the ultrasound acquisitions using a three-chamber alignment algorithm, simulated and measured flows were quantitatively compared. General flow pattern correspondence was observed, with a mean error of 1.4 cm/s and root mean square deviation of 5.7 cm/s for all measured PC-MRI LV-planes. For the PW-Doppler comparison, a mean error of 3.6 cm/s was reported. Overall, the following work represents a validation of the proposed patient-specific CFD platform, and the agreement with clinical data highlight the potential for future clinical use of the models.

  • 73.
    Laure, Erwin
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Kao, O.
    Badia, R. M.
    Lefevre, L.
    Di Martino, B.
    Prodan, R.
    Turilli, M.
    Warneke, D.
    Topic 6: Grid, cluster and cloud computing (Introduction)2013Ingår i: Lecture Notes in Computer Science, 2013, s. 241-Konferensbidrag (Refereegranskat)
    Abstract [en]

    Grid and cloud computing have changed the IT landscape in the way we access and manage IT infrastructures. The use of computing resources has become essential for many applications in various areas. Both technologies provide easyto- use and on-demand access to large-scale infrastructures. The high number of submissions to "Topic 6: Grid, Cluster and Cloud Computing" reflected the importance of the research area. The papers addressed key challenges regarding design, deployment, operation and use of Grid and cloud infrastructures. Moreover, several innovative algorithms and methods for fundamental capabilities and services that are required in a heterogeneous environment, such as adaptability, scalability, reliability and security, and to support applications as diverse as ubiquitous local services, enterprise-scale virtual organizations, and internet-scale distributed supercomputing were proposed. Finally, many experimental evaluations and use-cases delivered an insight into the deployment in real-world scenarios and showed interesting future application domains. Each submission was reviewed by at least four reviewers and, finally, we were able to select nine high-quality papers. The papers were grouped in four sessions that are briefly summarized in following.

  • 74.
    Laure, Erwin
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Vitlacil, Dejan
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Data storage and management for global research data infrastructures - Status and perspectives2013Ingår i: Data Science Journal, ISSN 1683-1470, E-ISSN 1683-1470, Vol. 12, s. GRD37-GRDI42Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In the vision of Global Research Data Infrastructures (GRDIs), data storage and management plays a crucial role. A successful GRDI will require a common globally interoperable distributed data system, formed out of data centres, that incorporates emerging technologies and new scientific data activities. The main challenge is to define common certification and auditing frameworks that will allow storage providers and data communities to build a viable partnership based on trust. To achieve this, it is necessary to find a long-term commitment model that will give financial, legal, and organisational guarantees of digital information preservation. In this article we discuss the state of the art in data storage and management for GRDIs and point out future research directions that need to be tackled to implement GRDIs.

  • 75. Leithinger, D.
    et al.
    Follmer, S.
    Olwal, Alex
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). Google (X)Mountain View, United States .
    Ishii, H.
    Physical Telepresence: Shape capture and display for embodied, computer-mediated remote collaboration2014Ingår i: UIST 2014 - Proceedings of the 27th Annual ACM Symposium on User Interface Software and Technology, Association for Computing Machinery (ACM), 2014, s. 461-470Konferensbidrag (Refereegranskat)
    Abstract [en]

    We propose a new approach to Physical Telepresence, based on shared workspaces with the ability to capture and remotely render the shapes of people and objects. In this paper, we describe the concept of shape transmission, and propose interaction techniques to manipulate remote physical objects and physical renderings of shared digital content. We investigate how the representation of user's body parts can be altered to amplify their capabilities for teleoperation. We also describe the details of building and testing prototype Physical Telepresence workspaces based on shape displays. A preliminary evaluation shows how users are able to manipulate remote objects, and we report on our observations of several different manipulation techniques that highlight the expressive nature of our system.

  • 76. Leithinger, Daniel
    et al.
    Follmer, Sean
    Olwal, Alex
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). Massachusetts Institute of Technology, United States.
    Ishii, Hiroshi
    Shape Displays: Spatial Interaction with Dynamic Physical Form2015Ingår i: IEEE Computer Graphics and Applications, ISSN 0272-1716, E-ISSN 1558-1756, Vol. 35, nr 5, s. 5-11Artikel i tidskrift (Refereegranskat)
  • 77.
    Li, Xiaopeng
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Playful Advertising: In-Game Advertising for Virtual Reality Games2015Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [sv]

    Vi presenterar en tidig utforskning av reklam i spelet för virtuell verklighet-spel. Studien undersöker hur interaktivitet och inlevelse påverkar konsumentlärande och - spelupplevelse. Först etableras en teoretisk grund för att förstå interaktivitet och inlevelse i virtuella spelmiljöer. Sedan skapas ett ramverk för forskning samt hypoteser kring frågeställningen. Sedan rapporterar vi resultaten från fältforskning, prototyp och användarstudie. Prototyperna körs i mobila webbläsare och testas på virtuell verklighet- glasögon med smartphones inuti. Baserat på resultaten, diskuteras utformning av interaktivitet och inlevelse, dess effekter på konsumentlärande och -spelupplevelse, samt sambandet mellan spelupplevelse och konsumentlärande. De viktigaste bidragen från arbetet är ett ramverk för forskning och en uppsättning av designöverväganden som kan användas för att utvärdera och förbättra effektiviteten hos reklam i virtuell verklighet-spel.

  • 78. Mancini, M.
    et al.
    Ermilov, A.
    Castellano, G.
    Liarokapis, F.
    Varni, G.
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Effects of gender mapping on the perception of emotion from upper body movement in virtual characters2014Ingår i: 6th International Conference on Virtual, Augmented and Mixed Reality, VAMR 2014 - Held as Part of 16th International Conference on Human-Computer Interaction, HCI International 2014, 2014, nr PART 1, s. 263-273Konferensbidrag (Refereegranskat)
    Abstract [en]

    Despite recent advancements in our understanding of the human perception of the emotional behaviour of embodied artificial entities in virtual reality environments, little remains known about various specifics relating to the effect of gender mapping on the perception of emotion from body movement. In this paper, a pilot experiment is presented investigating the effects of gender congruency on the perception of emotion from upper body movements. Male and female actors were enrolled to conduct a number of gestures within six general categories of emotion. These motions were mapped onto virtual characters with male and female embodiments. According to the gender congruency condition, the motions of male actors were mapped onto male characters (congruent) or onto female characters (incongruent) and vice-versa. A significant effect of gender mapping was found in the ratings of perception of three emotions (anger, fear and happiness), suggesting that gender may be an important aspect to be considered in the perception, and hence generation, of some emotional behaviours.

  • 79. Marchand, R.
    et al.
    Miyake, Y.
    Usui, H.
    Deca, J.
    Lapenta, G.
    Mateo-Velez, J. C.
    Ergun, R. E.
    Sturner, A.
    Genot, V.
    Hilgers, A.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Cross-comparison of spacecraft-environment interaction model predictions applied to Solar Probe Plus near perihelion2014Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 21, nr 6, s. 062901-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Five spacecraft-plasma models are used to simulate the interaction of a simplified geometry Solar Probe Plus (SPP) satellite with the space environment under representative solar wind conditions near perihelion. By considering similarities and differences between results obtained with different numerical approaches under well defined conditions, the consistency and validity of our models can be assessed. The impact on model predictions of physical effects of importance in the SPP mission is also considered by comparing results obtained with and without these effects. Simulation results are presented and compared with increasing levels of complexity in the physics of interaction between solar environment and the SPP spacecraft. The comparisons focus particularly on spacecraft floating potentials, contributions to the currents collected and emitted by the spacecraft, and on the potential and density spatial profiles near the satellite. The physical effects considered include spacecraft charging, photoelectron and secondary electron emission, and the presence of a background magnetic field. Model predictions obtained with our different computational approaches are found to be in agreement within 2% when the same physical processes are taken into account and treated similarly. The comparisons thus indicate that, with the correct description of important physical effects, our simulation models should have the required skill to predict details of satellite-plasma interaction physics under relevant conditions, with a good level of confidence. Our models concur in predicting a negative floating potential V-fl similar to -10V for SPP at perihelion. They also predict a "saturated emission regime" whereby most emitted photo-and secondary electron will be reflected by a potential barrier near the surface, back to the spacecraft where they will be recollected.

  • 80.
    Markidis, Markidis
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Lapenta, G.
    Delzanno, G. L.
    Henri, P.
    Goldman, M. V.
    Newman, D. L.
    Intrator, T.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Signatures of secondary collisionless magnetic reconnection driven by kink instability of a flux rope2014Ingår i: Plasma Physics and Controlled Fusion, ISSN 0741-3335, E-ISSN 1361-6587, Vol. 56, nr 6, s. 064010-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The kinetic features of secondary magnetic reconnection in a single flux rope undergoing internal kink instability are studied by means of three-dimensional particle-in-cell simulations. Several signatures of secondary magnetic reconnection are identified in the plane perpendicular to the flux rope: a quadrupolar electron and ion density structure and a bipolar Hall magnetic field develop in proximity of the reconnection region. The most intense electric fields form perpendicularly to the local magnetic field, and a reconnection electric field is identified in the plane perpendicular to the flux rope. An electron current develops along the reconnection line, in the opposite direction of the electron current supporting the flux rope magnetic field structure. Along the reconnection line, several bipolar structures of the electric field parallel to the magnetic field occur, making the magnetic reconnection region turbulent. The reported signatures of secondary magnetic reconnection can help to localize magnetic reconnection events in space, astrophysical and fusion plasmas.

  • 81.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Hart, Alistair
    Henty, David
    Heisey, Katherine
    Fischer, Paul
    OpenACC acceleration of the Nek5000 spectral element code2015Ingår i: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 29, nr 3, s. 311-319Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We present a case study of porting NekBone, a skeleton version of the Nek5000 code, to a parallel GPU-accelerated system. Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flow. The original NekBone Fortran source code has been used as the base and enhanced by OpenACC directives. The profiling of NekBone provided an assessment of the suitability of the code for GPU systems, and indicated possible kernel optimizations. To port NekBone to GPU systems required little effort and a small number of additional lines of code (approximately one OpenACC directive per 1000 lines of code). The naïve implementation using OpenACC leads to little performance improvement: on a single node, from 16 Gflops obtained with the version without OpenACC, we reached 20 Gflops with the naïve OpenACC implementation. An optimized NekBone version leads to a 43 Gflop performance on a single node. In addition, we ported and optimized NekBone to parallel GPU systems, reaching a parallel efficiency of 79.9% on 1024 GPUs of the Titan XK7 supercomputer at the Oak Ridge National Laboratory.

  • 82.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Henri, P.
    Lapenta, G.
    Divin, A.
    Goldman, M.
    Newman, D.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Kinetic simulations of plasmoid chain dynamics2013Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 20, nr 8, s. 082105-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The dynamics of a plasmoid chain is studied with three dimensional Particle-in-Cell simulations. The evolution of the system with and without a uniform guide field, whose strength is 1/3 the asymptotic magnetic field, is investigated. The plasmoid chain forms by spontaneous magnetic reconnection: the tearing instability rapidly disrupts the initial current sheet generating several small-scale plasmoids that rapidly grow in size coalescing and kinking. The plasmoid kink is mainly driven by the coalescence process. It is found that the presence of guide field strongly influences the evolution of the plasmoid chain. Without a guide field, a main reconnection site dominates and smaller reconnection regions are included in larger ones, leading to an hierarchical structure of the plasmoid-dominated current sheet. On the contrary in presence of a guide field, plasmoids have approximately the same size and the hierarchical structure does not emerge, a strong core magnetic field develops in the center of the plasmoid in the direction of the existing guide field, and bump-on-tail instability, leading to the formation of electron holes, is detected in proximity of the plasmoids.

  • 83.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Henri, Pierre
    Lapenta, Giovanni
    Ronnmark, Kjell
    Hamrin, Maria
    Meliani, Zakaria
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    The Fluid-Kinetic Particle-in-Cell method for plasma simulations2014Ingår i: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 271, s. 415-429Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A method that solves concurrently the multi-fluid and Maxwell's equations has been developed for plasma simulations. By calculating the stress tensor in the multi-fluid momentum equation by means of computational particles moving in a self-consistent electromagnetic field, the kinetic effects are retained while solving the multi-fluid equations. The Maxwell's and multi-fluid equations are discretized implicitly in time enabling kinetic simulations over time scales typical of the fluid simulations. The Fluid-Kinetic Particle-in-Cell method has been implemented in a three-dimensional electromagnetic code, and tested against the two-stream instability, the Weibel instability, the ion cyclotron resonance and magnetic reconnection problems. The method is a promising approach for coupling fluid and kinetic methods in a unified framework.

  • 84.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Solving software challenges for exascale: International Conference on Exascale Applications and Software, EASC 2014 Stockholm, Sweden, April 2–3, 2014 revised selected papers2015Ingår i: International Conference on Exascale Applications and Software, EASC 2014, Elsevier, 2015, Vol. 8759Konferensbidrag (Refereegranskat)
  • 85.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Aguilar, Xavier
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Henty, David
    University of Edinburgh.
    Richardson, Harvey
    Cray Inc..
    Hart, Alistair
    Cray Inc..
    Gray, Alan
    University of Edinburgh.
    Lecomber, David
    Allinea Software Limited.
    Hilbrich, Tobias
    Technische Universität Dresden.
    Doleschal, Jens
    Technische Universität Dresden.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Paving the path to exascale computing with CRESTA development environment2013Konferensbidrag (Övrigt vetenskapligt)
    Abstract [en]

    The development and implementation of efficient computer codes for exascale supercomputers will require combined advancement of all development environment components: compilers, automatic tuning frameworks, run-time systems, debuggers and performance monitoring and analysis tools. The exascale era poses unprecedented challenges. Because the presence of accelerators is more and more common among the fastest supercomputer and will play a role in exascale computing, compilers will need to support hybrid computer architectures and generate efficient code hiding the complexity of programming accelerators. Hand optimization of the code will be very difficult on exascale machine and will be increasingly assisted by automatic tuners. Application tuning will be more focus on parallel aspects of the computation because of large amount of available parallelism. The application workload will be distributed over million of processes, and to implement ad-hoc strategies directly in the application will be probably unfeasible while an adaptive run-time system will provide automatic load balancing. Debuggers and performance monitoring tools will deal with million processes and with huge amount of data from application and hardware counters, but they will still be required to minimize the overhead and retain scalability. In this talk, we present how the development environment of the CRESTA exascale EC project meets all these challenges by advancing the state of the art in the field.

    An investigation of compiler support for hybrid GPU programming, the design concepts, and the main characteristics of the alpha prototype implementation of the CRESTA development environment components for exascale computing are presented. A performance study of OpenACC compiler directives has been carried out, showing very promising results and indicating OpenACC as viable approach for programming hybrid exascale supercomputer. A new Domain-Specific Language (DSL) has been defined for the expression of parallel auto-tuning at very large scale. The focus of on the extension of the auto-tuning approach into the parallel domain to enable tuning of communication-related aspects of application. A new adaptive run-time system has been designed to schedule processes depending on the resource availability, on the workload, and on the run-time analysis of the application performance. The Allinea DDT debugger and the Dresden University of Technology MUST MPI correctness checker are being extended to provide a unified interface, to improve scalability, and to include new disruptive technology based on statistical analysis of run-time behavior of the application for anomalies detection. The new exascale prototypes of the Dresden University of Technology Vampir, VampirTrace and Score-P performance monitoring and analysis tools have been released. The new features include the possibility of applying filtering technique before loading performance data to drastically reduce memory needs during the performance analysis. The initial evaluation study of the development environment is targeted on the CRESTA project applications to determine how the development environment could be coupled into a production suite for exascale computing.

  • 86.
    Markidis, Stefano
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Vencels, Juris
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Peng, Ivy Bo
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Akhmetova, Dana
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Henri, Pierre
    Idle waves in high-performance computing2015Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 91, nr 1, s. 013306-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The vast majority of parallel scientific applications distributes computation among processes that are in a busy state when computing and in an idle state when waiting for information from other processes. We identify the propagation of idle waves through processes in scientific applications with a local information exchange between the two processes. Idle waves are nondispersive and have a phase velocity inversely proportional to the average busy time. The physical mechanism enabling the propagation of idle waves is the local synchronization between two processes due to remote data dependency. This study provides a description of the large number of processes in parallel scientific applications as a continuous medium. This work also is a step towards an understanding of how localized idle periods can affect remote processes, leading to the degradation of global performance in parallel scientific applications.

  • 87.
    Netzer, Gilbert
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Johnsson, Lennart
    University of Houston.
    Ahlin, Daniel
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC. KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Instrumentation for accurate energy-to-solution measurements of a texas instruments TMS320C6678 digital signal processor and its DDR3 memory2014Ingår i: E2SC ’14: Proceedings of the 2nd International Workshop on Energy Efficient Supercomputing, 2014, s. 89-98Konferensbidrag (Refereegranskat)
    Abstract [en]

    Architectural choices for High-Performance Computingsystems have once again become interesting with energyefficiency for targeted workloads now being a major decisionfactor. A detailed understanding of the energy consumptionof major system components during code execution is criticalfor evolving architectures towards enhanced energy efficiency.The focus of this paper is on the measurement system hard- and software we designed and implemented for the assessmentof the energy-to-solution of HPC workloads for the Texas Instruments TMS320C6678 (6678) Digital Signal Processor. The 6678’s thermal design power falls between x86 serverprocessors and mobile CPUs and so does its floating-pointand memory system capabilities. Yet, compared to those types of processors in corresponding CMOS technology, it offers a potentially significant energy advantage. The measurement system is described together with a thorough error analysis. Measurements are processed out-of-band minimizing the impact on the measured system. Sample observations of the energy efficiency of the 6678 and its memory system are included for illustration.

  • 88. O'Connor, S.
    et al.
    Liarokapis, F.
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    A perceptual study into the behaviour of autonomous agents within a virtual urban environment2013Ingår i: 2013 IEEE 14th International Symposium on a World of Wireless, Mobile and Multimedia Networks, WoWMoM 2013, IEEE , 2013, s. 6583494-Konferensbidrag (Refereegranskat)
    Abstract [en]

    Simulating vast crowds of autonomous agents within a procedurally generated virtual environment is a challenging endeavour from a technical perspective, however it becomes even more difficult when the subjective nature of perception is also taken into account. Agent behaviour is the product of artificial intelligence systems working in tandem, however the sophistication of these systems is not a guarantee of achieving believable behaviour. Within locations based upon reality such as an urban environment, the perceived realism of agent behaviour becomes even harder to achieve. This paper presents the development of a crowd simulation that is based upon a real-life urban environment, which is then subjected to perceptual experimentation to identify features of behaviour which can be linked to perceived realism. This research is predicted to feedback into the development processes of inhabited cities, especially those attempting to simulate perceptually realistic agents as it will highlight features of behaviour that are important to implement. The perceptual experimentation methodologies presented can also be adapted and potentially utilised to test other types of crowd simulation, whether it be for the purposes of computer games or even urban planning and health and safety.

  • 89. O'Connor, S.
    et al.
    Liarokapis, F.
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    An initial study to assess the perceived realism of agent crowd behaviour in a virtual city2013Ingår i: Int. Conf. Games Virtual Worlds Serious Appl., VS-GAMES, 2013Konferensbidrag (Refereegranskat)
    Abstract [en]

    This paper examines the development of a crowd simulation in a virtual city, and a perceptual experiment to identify features of behaviour which can be linked to perceived realism. This research is expected to feedback into the development processes of simulating inhabited locations, by identifying the key features which need to be implemented to achieve more perceptually realistic crowd behaviour. The perceptual experimentation methodologies presented can be adapted and potentially utilised to test other types of crowd simulation, for application within computer games or more specific simulations such as for urban planning or health and safety purposes.

  • 90. Olshevsky, V.
    et al.
    Lapenta, G.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Energetics of Kinetic Reconnection in a Three-Dimensional Null-Point Cluster2013Ingår i: Physical Review Letters, ISSN 0031-9007, E-ISSN 1079-7114, Vol. 111, nr 4, s. 045002-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We perform three-dimensional particle-in-cell simulations of magnetic reconnection with multiple magnetic null points. Magnetic field energy conversion into kinetic energy is about five times higher than in traditional Harris sheet configuration. More than 85% of initial magnetic field energy is transferred to particle energy during 25 reversed ion cyclofrequencies. Magnetic reconnection in the cluster of null points evolves in three phases. During the first phase, ion beams are excited, then give part of their energy back to the magnetic field in the second phase. In the third phase, magnetic reconnection occurs in many small patches around the current channels formed along the stripes of a low magnetic field. Magnetic reconnection in null points essentially presents three-dimensional features, with no two-dimensional symmetries or current sheets.

  • 91. Olshevsky, Vyacheslav
    et al.
    Divin, Andrey
    Eriksson, Elin
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Lapenta, Giovanni
    ENERGY DISSIPATION IN MAGNETIC NULL POINTS AT KINETIC SCALES2015Ingår i: Astrophysical Journal, ISSN 0004-637X, E-ISSN 1538-4357, Vol. 807, nr 2, artikel-id 155Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We use kinetic particle-in-cell and MHD simulations supported by an observational data set to investigate magnetic reconnection in clusters of null points in space plasma. The magnetic configuration under investigation is driven by fast adiabatic flux rope compression that dissipates almost half of the initial magnetic field energy. In this phase powerful currents are excited producing secondary instabilities, and the system is brought into a state of "intermittent turbulence" within a few ion gyro-periods. Reconnection events are distributed all over the simulation domain and energy dissipation is rather volume-filling. Numerous spiral null points interconnected via their spines form null lines embedded into magnetic flux ropes; null point pairs demonstrate the signatures of torsional spine reconnection. However, energy dissipation mainly happens in the shear layers formed by adjacent flux ropes with oppositely directed currents. In these regions radial null pairs are spontaneously emerging and vanishing, associated with electron streams and small-scale current sheets. The number of spiral nulls in the simulation outweighs the number of radial nulls by a factor of 5-10, in accordance with Cluster observations in the Earth's magnetosheath. Twisted magnetic fields with embedded spiral null points might indicate the regions of major energy dissipation for future space missions such as the Magnetospheric Multiscale Mission.

  • 92. Olshevsky, Vyacheslav
    et al.
    Lapenta, Giovanni
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Divin, Andrey
    Role of Z-pinches in magnetic reconnection in space plasmas2015Ingår i: Journal of Plasma Physics, ISSN 0022-3778, E-ISSN 1469-7807, Vol. 81, nr 1, artikel-id 325810105Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A widely accepted scenario of magnetic reconnection in collisionless space plasmas is the breakage of magnetic field lines in X-points. In laboratory, reconnection is commonly studied in pinches, current channels embedded into twisted magnetic fields. No model of magnetic reconnection in space plasmas considers both nullpoints and pinches as peers. We have performed a particle-in-cell simulation of magnetic reconnection in a three-dimensional configuration where null-points are present initially, and Z-pinches are formed during the simulation along the lines of spiral null-points. The non-spiral null-points are more stable than spiral ones, and no substantial energy dissipation is associated with them. On the contrary, turbulent magnetic reconnection in the pinches causes the magnetic energy to decay at a rate of similar to 1.5% per ion gyro period. Dissipation in similar structures is a likely scenario in space plasmas with large fraction of spiral null-points.

  • 93.
    Olwal, Alex
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    DiVerdi, S.
    Candussi, N.
    Rakkolainen, I.
    Höllerer, T.
    An immaterial, dual-sided display system with 3D interaction2006Ingår i: Proc. IEEE Virtual Real., 2006Konferensbidrag (Refereegranskat)
    Abstract [en]

    We present an interactive wall-sized immaterial display that introduces a number of interesting possibilities for advanced interface design. The immaterial nature of a thin sheet of fog allows users to penetrate and even walk through the screen, while its dual-sided nature allows for new possibilities in multi-user face-to-face collaboration and pseudo-3D visualization.

  • 94.
    Olwal, Alex
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Höllerer, T.
    POLAR: Portable, optical see-through, low-cost augmented reality2006Ingår i: Proc. ACM Symp. Virtual Reality Softw. Technol. VRST, 2006, s. 227-230Konferensbidrag (Refereegranskat)
    Abstract [en]

    We describe POLAR, a portable, optical see-through, low-cost augmented reality system, which allows a user to see annotated views of small to medium-sized physical objects in an unencumbered way. No display or tracking equipment needs to be worn. We describe the system design, including a hybrid IR/vision head-tracking solution, and present examples of simple augmented scenes. POLAR's compactness could allow it to be used as a lightweight and portable PC peripheral for providing mobile users with on-demand AR access in field work.

  • 95. Paetzel, M.
    et al.
    Hupont, I.
    Varni, G.
    Chetouani, M.
    Peters, Christopher
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz). KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Castellano, G.
    Exploring the link between self-assessed mimicry and embodiment in HRI2017Ingår i: ACM/IEEE International Conference on Human-Robot Interaction, IEEE Computer Society , 2017, s. 245-246Konferensbidrag (Refereegranskat)
    Abstract [en]

    This work explores the relationship between a robot's embodiment and people's ability to mimic its behavior. It presents a study in which participants were asked to mimic a 3D mixed-embodied robotic head and a 2D version of the same character. Quantitative and qualitative analysis were performed from questionnaires. Quantitative results show no significant influence of the character's embodiment on the self-assessed ability to mimic it, while qualitative ones indicate a preference for mimicking the robotic head.

  • 96.
    Peng, Bo
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Vaivads, A.
    Vencels, Juris
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Amaya, J.
    Divin, A.
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Lapenta, G.
    The formation of a magnetosphere with implicit Particle-in-Cell simulations2015Ingår i: Procedia Computer Science, Elsevier, 2015, nr 1, s. 1178-1187Konferensbidrag (Refereegranskat)
    Abstract [en]

    We demonstrate the improvements to an implicit Particle-in-Cell code, iPic3D, on the example of dipolar magnetic field immersed in the flow of the plasma and show the formation of a magnetosphere. We address the problem of modelling multi-scale phenomena during the formation of a magnetosphere by implementing an adaptive sub-cycling technique to resolve the motion of particles located close to the magnetic dipole centre, where the magnetic field intensity is maximum. In addition, we implemented new open boundary conditions to model the inflow and outflow of plasma. We present the results of a global three-dimensional Particle-in-Cell simulation and discuss the performance improvements from the adaptive sub-cycling technique.

  • 97.
    Peng, I. Bo
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Johlander, A.
    Vaivads, A.
    Khotyaintsev, Y.
    Henri, P.
    Lapenta, G.
    Kinetic structures of quasi-perpendicular shocks in global particle-in-cell simulations2015Ingår i: Physics of Plasmas, ISSN 1070-664X, E-ISSN 1089-7674, Vol. 22, nr 9, artikel-id 092109Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We carried out global Particle-in-Cell simulations of the interaction between the solar wind and a magnetosphere to study the kinetic collisionless physics in super-critical quasi-perpendicular shocks. After an initial simulation transient, a collisionless bow shock forms as a result of the interaction of the solar wind and a planet magnetic dipole. The shock ramp has a thickness of approximately one ion skin depth and is followed by a trailing wave train in the shock downstream. At the downstream edge of the bow shock, whistler waves propagate along the magnetic field lines and the presence of electron cyclotron waves has been identified. A small part of the solar wind ion population is specularly reflected by the shock while a larger part is deflected and heated by the shock. Solar wind ions and electrons are heated in the perpendicular directions. Ions are accelerated in the perpendicular direction in the trailing wave train region. This work is an initial effort to study the electron and ion kinetic effects developed near the bow shock in a realistic magnetic field configuration.

  • 98.
    Peng, Ivy Bo
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Vencels, Juris
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Lapenta, Giovanni
    Divin, Andrey
    Vaivads, Andris
    Laure, Erwin
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Energetic particles in magnetotail reconnection2015Ingår i: Journal of Plasma Physics, ISSN 0022-3778, E-ISSN 1469-7807, Vol. 81, artikel-id 325810202Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We carried out a 3D fully kinetic simulation of Earth's magnetotail magnetic reconnection to study the dynamics of energetic particles. We developed and implemented a new relativistic particle mover in iPIC3D, an implicit Particle-in-Cell code, to correctly model the dynamics of energetic particles. Before the onset of magnetic reconnection, energetic electrons are found localized close to current sheet and accelerated by lower hybrid drift instability. During magnetic reconnection, energetic particles are found in the reconnection region along the x-line and in the separatrices region. The energetic electrons are first present in localized stripes of the separatrices and finally cover all the separatrix surfaces. Along the separatrices, regions with strong electron deceleration are found. In the reconnection region, two categories of electron trajectory are identified. First, part of the electrons are trapped in the reconnection region, bouncing a few times between the outflow jets. Second, part of the electrons pass the reconnection region without being trapped. Different from electrons, energetic ions are localized on the reconnection fronts of the outflow jets.

  • 99.
    Peters, Christopher E.
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Anderson, Eike Falk
    Bournemouth University.
    The Four I's Recipe for Cooking Up Computer Graphics Exercises and Assessments2014Konferensbidrag (Refereegranskat)
    Abstract [en]

    The design of meaningful student activities, such as lab exercises and assignments, is a core element of computer graphics pedagogy. Here, we briefly describe our efforts towards making the process of defining and structuring computer graphics activities more explicit. We focus on four main activity categories that are building blocks for practical course design: Independent, Iterative, Incremental and Integrative. These ``Four I's'' of computer graphics activity provide the fundamental ingredients for explicitly defining the design of activity-oriented computer graphics courses with the potential to deliver significant artefacts that may, for example, constitute a portfolio of work for assessment or presentation to employers. The categorisations are intended as the first steps towards more clearly structuring and communicating exercise specifications in collaborative course development settings.

  • 100.
    Peters, Christopher E.
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Kjelldahl, LarsKTH, Skolan för datavetenskap och kommunikation (CSC).
    SIGRAD 2015: Proceedings of the annual meeting of the Swedish Computer Graphics Association (SIGRAD)2015Proceedings (redaktörskap) (Refereegranskat)
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