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  • 101.
    Thoman, Peter
    et al.
    Univ Innsbruck, A-6020 Innsbruck, Austria..
    Dichev, Kiril
    Queens Univ Belfast, Belfast BT7 1NN, Antrim, North Ireland..
    Heller, Thomas
    Univ Erlangen Nurnberg, D-91058 Erlangen, Germany..
    Iakymchuk, Roman
    KTH.
    Aguilar, Xavier
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Hasanov, Khalid
    IBM Ireland, Dublin 15, Ireland..
    Gschwandtner, Philipp
    Univ Innsbruck, A-6020 Innsbruck, Austria..
    Lemarinier, Pierre
    IBM Ireland, Dublin 15, Ireland..
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Jordan, Herbert
    Univ Innsbruck, A-6020 Innsbruck, Austria..
    Fahringer, Thomas
    Univ Innsbruck, A-6020 Innsbruck, Austria..
    Katrinis, Kostas
    IBM Ireland, Dublin 15, Ireland..
    Laure, Erwin
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Nikolopoulos, Dimitrios S.
    Queens Univ Belfast, Belfast BT7 1NN, Antrim, North Ireland..
    A taxonomy of task-based parallel programming technologies for high-performance computing2018Inngår i: Journal of Supercomputing, ISSN 0920-8542, E-ISSN 1573-0484, Vol. 74, nr 4, s. 1422-1434Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Task-based programming models for shared memory-such as Cilk Plus and OpenMP 3-are well established and documented. However, with the increase in parallel, many-core, and heterogeneous systems, a number of research-driven projects have developed more diversified task-based support, employing various programming and runtime features. Unfortunately, despite the fact that dozens of different task-based systems exist today and are actively used for parallel and high-performance computing (HPC), no comprehensive overview or classification of task-based technologies for HPC exists. In this paper, we provide an initial task-focused taxonomy for HPC technologies, which covers both programming interfaces and runtime mechanisms. We demonstrate the usefulness of our taxonomy by classifying state-of-the-art task-based environments in use today.

  • 102.
    Thoman, Peter
    et al.
    Univ Innsbruck, Innsbruck, Austria..
    Hasanov, Khalid
    IBM Ireland, Dublin, Ireland..
    Dichev, Kiril
    Queens Univ Belfast, Belfast, Antrim, North Ireland..
    Iakymchuk, Roman
    KTH.
    Aguilar, Xavier
    KTH.
    Gschwandtner, Philipp
    Univ Innsbruck, Innsbruck, Austria..
    Lemarinier, Pierre
    IBM Ireland, Dublin, Ireland..
    Markidis, Stefano
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST).
    Jordan, Herbert
    Univ Innsbruck, Innsbruck, Austria..
    Laure, Erwin
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST).
    Katrinis, Kostas
    IBM Ireland, Dublin, Ireland..
    Nikolopoulos, Dimitrios S.
    Queens Univ Belfast, Belfast, Antrim, North Ireland..
    Fahringer, Thomas
    Univ Innsbruck, Innsbruck, Austria..
    A Taxonomy of Task-Based Technologies for High-Performance Computing2018Inngår i: PARALLEL PROCESSING AND APPLIED MATHEMATICS (PPAM 2017), PT II / [ed] Wyrzykowski, R Dongarra, J Deelman, E Karczewski, K, SPRINGER INTERNATIONAL PUBLISHING AG , 2018, s. 264-274Konferansepaper (Fagfellevurdert)
    Abstract [en]

    Task-based programming models for shared memory - such as Cilk Plus and OpenMP 3 - are well established and documented. However, with the increase in heterogeneous, many-core and parallel systems, a number of research-driven projects have developed more diversified task-based support, employing various programming and runtime features. Unfortunately, despite the fact that dozens of different task-based systems exist today and are actively used for parallel and high-performance computing, no comprehensive overview or classification of task-based technologies for HPC exists. In this paper, we provide an initial task-focused taxonomy for HPC technologies, which covers both programming interfaces and runtime mechanisms. We demonstrate the usefulness of our taxonomy by classifying state-of-the-art task-based environments in use today.

  • 103. Toth, Gabor
    et al.
    Chen, Yuxi
    Gombosi, Tamas I.
    Cassak, Paul
    Markidis, Stefano
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Peng, Ivy Bo
    KTH.
    Scaling the Ion Inertial Length and Its Implications for Modeling Reconnection in Global Simulations2017Inngår i: Journal of Geophysical Research - Space Physics, ISSN 2169-9380, E-ISSN 2169-9402, Vol. 122, nr 10, s. 10336-10355Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We investigate the use of artificially increased ion and electron kinetic scales in global plasma simulations. We argue that as long as the global and ion inertial scales remain well separated, (1) the overall global solution is not strongly sensitive to the value of the ion inertial scale, while (2) the ion inertial scale dynamics will also be similar to the original system, but it occurs at a larger spatial scale, and (3) structures at intermediate scales, such as magnetic islands, grow in a self-similar manner. To investigate the validity and limitations of our scaling hypotheses, we carry out many simulations of a two-dimensional magnetosphere with the magnetohydrodynamics with embedded particle-in-cell (MHD-EPIC) model. The PIC model covers the dayside reconnection site. The simulation results confirm that the hypotheses are true as long as the increased ion inertial length remains less than about 5% of the magnetopause standoff distance. Since the theoretical arguments are general, we expect these results to carry over to three dimensions. The computational cost is reduced by the third and fourth powers of the scaling factor in two-and three-dimensional simulations, respectively, which can be many orders of magnitude. The present results suggest that global simulations that resolve kinetic scales for reconnection are feasible. This is a crucial step for applications to the magnetospheres of Earth, Saturn, and Jupiter and to the solar corona.

  • 104. Toth, Gabor
    et al.
    Jia, Xianzhe
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Peng, Ivy Bo
    KTH, Skolan för datavetenskap och kommunikation (CSC), Beräkningsvetenskap och beräkningsteknik (CST).
    Chen, Yuxi
    Daldorff, Lars K. S.
    Tenishev, Valeriy M.
    Borovikov, Dmitry
    Haiducek, John D.
    Gombosi, Tamas I.
    Glocer, Alex
    Dorelli, John C.
    Extended magnetohydrodynamics with embedded particle-in-cell simulation of Ganymede's magnetosphere2016Inngår i: Journal of Geophysical Research - Space Physics, ISSN 2169-9380, E-ISSN 2169-9402, Vol. 121, nr 2, s. 1273-1293Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have recently developed a new modeling capability to embed the implicit particle-in-cell (PIC) model iPIC3D into the Block-Adaptive-Tree-Solarwind-Roe-Upwind-Scheme magnetohydrodynamic (MHD) model. The MHD with embedded PIC domains (MHD-EPIC) algorithm is a two-way coupled kinetic-fluid model. As one of the very first applications of the MHD-EPIC algorithm, we simulate the interaction between Jupiter's magnetospheric plasma and Ganymede's magnetosphere. We compare the MHD-EPIC simulations with pure Hall MHD simulations and compare both model results with Galileo observations to assess the importance of kinetic effects in controlling the configuration and dynamics of Ganymede's magnetosphere. We find that the Hall MHD and MHD-EPIC solutions are qualitatively similar, but there are significant quantitative differences. In particular, the density and pressure inside the magnetosphere show different distributions. For our baseline grid resolution the PIC solution is more dynamic than the Hall MHD simulation and it compares significantly better with the Galileo magnetic measurements than the Hall MHD solution. The power spectra of the observed and simulated magnetic field fluctuations agree extremely well for the MHD-EPIC model. The MHD-EPIC simulation also produced a few flux transfer events (FTEs) that have magnetic signatures very similar to an observed event. The simulation shows that the FTEs often exhibit complex 3-D structures with their orientations changing substantially between the equatorial plane and the Galileo trajectory, which explains the magnetic signatures observed during the magnetopause crossings. The computational cost of the MHD-EPIC simulation was only about 4 times more than that of the Hall MHD simulation. Key Points

  • 105. Vapirev, A.
    et al.
    Deca, J.
    Lapenta, G.
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), Centra, Parallelldatorcentrum, PDC.
    Hur, I.
    Cambier, J. -L
    Initial results on computational performance of Intel many integrated core, sandy bridge, and graphical processing unit architectures: implementation of a 1D c++/OpenMP electrostatic particle-in-cell code2015Inngår i: Concurrency and Computation, ISSN 1532-0626, E-ISSN 1532-0634, Vol. 27, nr 3, s. 581-593Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We present initial comparison performance results for Intel many integrated core (MIC), Sandy Bridge (SB), and graphical processing unit (GPU). A 1D explicit electrostatic particle-in-cell code is used to simulate a two-stream instability in plasma. We compare the computation times for various number of cores/threads and compiler options. The parallelization is implemented via OpenMP with a maximum thread number of 128. Parallelization and vectorization on the GPU is achieved with modifying the code syntax for compatibility with CUDA. We assess the speedup due to various auto-vectorization and optimization level compiler options. Our results show that the MIC is several times slower than SB for a single thread, and it becomes faster than SB when the number of cores increases with vectorization switched on. The compute times for the GPU are consistently about six to seven times faster than the ones for MIC. Compared with SB, the GPU is about two times faster for a single thread and about an order of magnitude faster for 128 threads. The net speedup, however, for MIC and GPU are almost the same. An initial attempt to offload parts of the code to the MIC coprocessor shows that there is an optimal number of threads where the speedup reaches a maximum.

  • 106. Vapirev, A. E.
    et al.
    Lapenta, G.
    Divin, A.
    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.
    Henri, P.
    Goldman, M.
    Newman, D.
    Formation of a transient front structure near reconnection point in 3-D PIC simulations2013Inngår i: Journal of Geophysical Research, ISSN 0148-0227, E-ISSN 2156-2202, Vol. 118, nr 4, s. 1435-1449Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Massively parallel numerical simulations of magnetic reconnection are presented in this study. Electromagnetic full-particle implicit code iPIC3D is used to study the dynamics and 3-D evolution of reconnection outflows. Such features as Hall magnetic field, inflow and outflow, and diffusion region formation are very similar to 2-D particle-in-cell (PIC) simulations. In addition, it is well known that instabilities develop in the current flow direction or oblique directions. These modes could provide for anomalous resistivity and diffusive drag and can serve as additional proxies for magnetic reconnection. In our work, the unstable evolution of reconnection transient front structures is studied. Reconnection configuration in the absence of guide field is considered, and it is initialized with a localized perturbation aligned in the cross-tail direction. Our study suggests that the instabilities lead to the development of finger-like density structures on ion-electron hybrid scales. These structures are characterized by a rapid increase of the magnetic field, normal to the current sheet (Bz). A small decrease in the magnetic field component parallel to the reconnection X line and the component perpendicular to the current sheet is observed in the region ahead of the front. The instabilities form due to fact that the density gradient inside the front region is opposite to the direction of the acceleration Lorentz force. Such density structures may possibly further develop into larger-scale earthward flux transfer events during magnetotail reconnection. In addition, oscillations mainly in the magnetic and electric fields and the electron density are observed shortly before the arrival of the main front structure which is consistent with recent THEMIS observations. Key PointsThree dimensional particle-in-cell simulation of reconnection in the magnetotailEvolution of dipolarization front at reconnection and associated plasma flowDevelopment of instabilities in the plasma population

  • 107.
    Vencels, Juris
    et al.
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Delzanno, G. L.
    Johnson, A.
    Peng, I. Bo
    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).
    Markidis, Stefano
    KTH, Skolan för datavetenskap och kommunikation (CSC), High Performance Computing and Visualization (HPCViz).
    Spectral solver for multi-scale plasma physics simulations with dynamically adaptive number of moments2015Inngår i: Procedia Computer Science, Elsevier, 2015, nr 1, s. 1148-1157Konferansepaper (Fagfellevurdert)
    Abstract [en]

    A spectral method for kinetic plasma simulations based on the expansion of the velocity distribution function in a variable number of Hermite polynomials is presented. The method is based on a set of non-linear equations that is solved to determine the coefficients of the Hermite expansion satisfying the Vlasov and Poisson equations. In this paper, we first show that this technique combines the fluid and kinetic approaches into one framework. Second, we present an adaptive strategy to increase and decrease the number of Hermite functions dynamically during the simulation. The technique is applied to the Landau damping and two-stream instability test problems. Performance results show 21% and 47% saving of total simulation time in the Landau and two-stream instability test cases, respectively.

  • 108.
    Wallden, Marcus
    et al.
    Osaka Univ, Grad Sch Informat Sci & Technol, Suita, Osaka 5650871, Japan..
    Markidis, Stefano
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Datavetenskap, Beräkningsvetenskap och beräkningsteknik (CST).
    Okita, Masao
    Osaka Univ, Grad Sch Informat Sci & Technol, Suita, Osaka 5650871, Japan..
    Ino, Fumihiko
    Osaka Univ, Grad Sch Informat Sci & Technol, Suita, Osaka 5650871, Japan..
    Memory Efficient Load Balancing for Distributed Large-Scale Volume Rendering Using a Two-Layered Group Structure2019Inngår i: IEICE transactions on information and systems, ISSN 0916-8532, E-ISSN 1745-1361, Vol. E102D, nr 12, s. 2306-2316Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We propose a novel compositing pipeline and a dynamic load balancing technique for volume rendering which utilizes a two-layered group structure to achieve effective and scalable load balancing. The technique enables each process to render data from non-contiguous regions of the volume with minimal impact on the total render time. We demonstrate the effectiveness of the proposed technique by performing a set of experiments on a modern GPU cluster. The experiments show that using the technique results in up to a 35.7% lower worst-case memory usage as compared to a dynamic k-d tree load balancing technique, whilst simultaneously achieving similar or higher render performance. The proposed technique was also able to lower the amount of transferred data during the load balancing stage by up to 72.2%. The technique has the potential to be used in many scenarios where other dynamic load balancing techniques have proved to be inadequate, such as during large-scale visualization.

  • 109.
    Yu, Yiqun
    et al.
    Beihang Univ, Sch Space & Environm, Beijing, Peoples R China..
    Delzanno, Gian Luca
    Los Alamos Natl Lab, Los Alamos, NM USA..
    Jordanova, Vania
    Los Alamos Natl Lab, Los Alamos, NM USA..
    Peng, Ivy Bo
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Centra, Parallelldatorcentrum, PDC.
    Markidis, Stefano
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST).
    PIC simulations of wave-particle interactions with an initial electron velocity distribution from a kinetic ring current model2018Inngår i: Journal of Atmospheric and Solar-Terrestrial Physics, ISSN 1364-6826, E-ISSN 1879-1824, Vol. 177, s. 169-178Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Whistler wave-particle interactions play an important role in the Earth inner magnetospheric dynamics and have been the subject of numerous investigations. By running a global kinetic ring current model (RAM-SCB) in a storm event occurred on Oct 23-24 2002, we obtain the ring current electron distribution at a selected location at MLT of 9 and L of 6 where the electron distribution is composed of a warm population in the form of a partial ring in the velocity space (with energy around 15 keV) in addition to a cool population with a Maxwellian-like distribution. The warm population is likely from the injected plasma sheet electrons during substorm injections that supply fresh source to the inner magnetosphere. These electron distributions are then used as input in an implicit particle-in-cell code (iPIC3D) to study whistler-wave generation and the subsequent wave-particle interactions. We find that whistler waves are excited and propagate in the quasi-parallel direction along the background magnetic field. Several different wave modes are instantaneously generated with different growth rates and frequencies. The wave mode at the maximum growth rate has a frequency around 0.62 omega(ce), which corresponds to a parallel resonant energy of 2.5 keV. Linear theory analysis of wave growth is in excellent agreement with the simulation results. These waves grow initially due to the injected warm electrons and are later damped due to cyclotron absorption by electrons whose energy is close to the resonant energy and can effectively attenuate waves. The warm electron population overall experiences net energy loss and anisotropy drop while moving along the diffusion surfaces towards regions of lower phase space density, while the cool electron population undergoes heating when the waves grow, suggesting the cross-population interactions.

  • 110.
    Zhou, Hongyang
    et al.
    Univ Michigan, Dept Climate & Space Sci & Engn, Ann Arbor, MI 48109 USA..
    Toth, Gabor
    Univ Michigan, Dept Climate & Space Sci & Engn, Ann Arbor, MI 48109 USA..
    Jia, Xianzhe
    Univ Michigan, Dept Climate & Space Sci & Engn, Ann Arbor, MI 48109 USA..
    Chen, Yuxi
    Univ Michigan, Dept Climate & Space Sci & Engn, Ann Arbor, MI 48109 USA..
    Markidis, Stefano
    KTH, Skolan för elektroteknik och datavetenskap (EECS), Beräkningsvetenskap och beräkningsteknik (CST).
    Embedded Kinetic Simulation of Ganymede's Magnetosphere: Improvements and Inferences2019Inngår i: Journal of Geophysical Research - Space Physics, ISSN 2169-9380, E-ISSN 2169-9402, Vol. 124, nr 7, s. 5441-5460Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The largest moon in the solar system, Ganymede, is also the only moon known to possess a strong intrinsic magnetic field and a corresponding magnetosphere. Using the new version of Hall magnetohydrodynamic with embedded particle-in-cell model with a self-consistently coupled resistive body representing the electrical properties of the moon's interior, improved inner boundary conditions, and the flexibility of coupling different grid geometries, we achieve better match of magnetic field with measurements for all six Galileo flybys. The G2 flyby comparisons of plasma bulk flow velocities with the Galileo Plasma Subsystem data support the oxygen ion assumption inside Ganymede's magnetosphere. Crescent shape, nongyrotropic, and nonisotropic ion distributions are identified from the coupled model. Furthermore, we have derived the energy fluxes associated with the upstream magnetopause reconnection of similar to 10(-7) W/cm(2) based on our model results and found a maximum of 40% contribution to the total peak auroral emissions.

123 101 - 110 of 110
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