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  • 1. Bongo, Lars Ailo
    et al.
    Ciegis, Raimondas
    Frasheri, Neki
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Kimovski, Dragi
    Kropf, Peter
    Margenov, Svetozar
    Mihajlovic, Milan
    Neytcheva, Maya
    Rauber, Thomas
    Rünger, Gudula
    Trobec, Roman
    Wuyts, Roel
    Wyrzykowski, Roman
    Applications for Ultrascale Computing2015In: Supercomputing Frontiers and Innovations, ISSN 2409-6008, Vol. 2, no 1, p. 19-48Article in journal (Refereed)
    Abstract [en]

    Studies of complex physical and engineering systems, represented by multi-scale and multi-physics computer simulations have an increasing demand for computing power, especially when the simulations of realistic problems are considered. This demand is driven by the increasing size and complexity of the studied systems or the time constraints. Ultrascale computing systems offer a possible solution to this problem. Future ultrascale systems will be large-scale complex computing systems combining technologies from high performance computing, distributed systems, big data, and cloud computing. Thus, the challenge of developing and programming complex algorithms on these systems is twofold. Firstly, the complex algorithms have to be either developed from scratch, or redesigned in order to yield high performance, while retaining correct functional behaviour. Secondly, ultrascale computing systems impose a number of non-functional cross-cutting concerns, such as fault tolerance or energy consumption, which can significantly impact the deployment of applications on large complex systems. This article discusses the state-of-the-art of programming for current and future large scale systems with an emphasis on complex applications. We derive a number of programming and execution support requirements by studying several computing applications that the authors are currently developing and discuss their potential and necessary upgrades for ultrascale execution.

  • 2.
    Efraimsson, Gunilla
    et al.
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering, Aeroacoustics.
    Gong, Jing
    IT-department, Uppsala University.
    Svärd, Magnus
    Stanford University, Standford, USA.
    Nordström, Jan
    IT-department, Uppsala University.
    An Investigation of the Performance of a High-Order Accurate Navier-Stokes Code2006In: ECCOMAS CFD 2006, 2006, p. 11-Conference paper (Refereed)
  • 3. Eliasson, P.
    et al.
    Gong, Jing
    KTH, School of Electrical Engineering and Computer Science (EECS), Centres, Centre for High Performance Computing, PDC.
    Nordström, J.
    A stable and conservative coupling of the unsteady compressible navier-stokes equations at interfaces using finite difference and finite volume methods2018In: AIAA Aerospace Sciences Meeting, 2018, American Institute of Aeronautics and Astronautics Inc, AIAA , 2018, no 210059Conference paper (Refereed)
    Abstract [en]

    Stable and conservative interface boundary conditions are developed for the unsteady compressible Navier-Stokes equations using finite difference and finite volume methods. The finite difference approach is based on summation-by-part operators and can be made higher order accurate with boundary conditions imposed weakly. The finite volume approach is an edge- and dual grid-based approach for unstructured grids, formally second order accurate in space, with weak boundary conditions as well. Stable and conservative weak boundary conditions are derived for interfaces between finite difference methods, for finite volume methods and for the coupling between the two approaches. The three types of interface boundary conditions are demonstrated for two test cases. Firstly, inviscid vortex propagation with a known analytical solution is considered. The results show expected error decays as the grid is refined for various couplings and spatial accuracy of the finite difference scheme. The second test case involves viscous laminar flow over a cylinder with vortex shedding. Calculations with various coupling and spatial accuracies of the finite difference solver show that the couplings work as expected and that the higher order finite difference schemes provide enhanced vortex propagation.

  • 4. Eriksson, Sofia
    et al.
    Law, Craig
    Gong, Jing
    Uppsala Univ. IT dept..
    Nordström, Jan
    Shock Calculations using a Very High Order Accurate Euler and Navier-Stokes Solver2008In: Proc. 6th South African Conference on Computational and Applied Mechanics, 2008, p. 63-73Conference paper (Refereed)
  • 5.
    Gong, Jing
    Uppsala University.
    Hybrid Methods for Unsteady Fluid Flow Problems in Complex Geometries2007Doctoral thesis, comprehensive summary (Other academic)
  • 6.
    Gong, Jing
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hart, Alistair
    Cray Inc..
    Henty, David
    University of Edinburgh.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Fischer, Paul
    Argonne National Laboratory.
    Heisey, Katherine
    Argonne National Laboratory.
    OpenACC Acceleration of Nek5000: a Spectral Element Code2013Conference paper (Other academic)
  • 7.
    Gong, Jing
    et al.
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Otten, Matthew
    Fischer, Paul
    Min, Misun
    Nekbone performance on GPUs with OpenACC and CUDA Fortran implementations2016In: Journal of Supercomputing, ISSN 0920-8542, E-ISSN 1573-0484, Vol. 72, no 11, p. 4160-4180Article in journal (Refereed)
    Abstract [en]

    We present a hybrid GPU implementation and performance analysis of Nekbone, which represents one of the core kernels of the incompressible Navier-Stokes solver Nek5000. The implementation is based on OpenACC and CUDA Fortran for local parallelization of the compute-intensive matrix-matrix multiplication part, which significantly minimizes the modification of the existing CPU code while extending the simulation capability of the code to GPU architectures. Our discussion includes the GPU results of OpenACC interoperating with CUDA Fortran and the gather-scatter operations with GPUDirect communication. We demonstrate performance of up to 552 Tflops on 16, 384 GPUs of the OLCF Cray XK7 Titan.

  • 8.
    Gong, Jing
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Cebamanos, Luis
    Hart, Alistair
    Min, Misun
    Fischer, Paul
    NekBone with Optimizaed OpenACC directives2015Conference paper (Refereed)
    Abstract [en]

    Accelerators and, in particular, Graphics Processing Units (GPUs) have emerged as promising computing technologies which may be suitable for the future Exascale systems. Here, we present performance results of NekBone, a benchmark of the Nek5000 code, implemented with optimized OpenACC directives and GPUDirect communications. Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flow. Results of an optimized NekBone version lead to 78 Gflops performance on a single node. In addition, a performance result of 609 Tflops has been reached on 16, 384 GPUs of the Titan supercomputer at Oak Ridge National Laboratory.

     

  • 9.
    Gong, Jing
    et al.
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Peplinski, Adam
    Hart, Alistair
    Doleschal, Jens
    Henty, David
    Fischer, Paul
    Nek5000 with OpenACC2015In: Solving software challenges for exascale, 2015, p. 57-68Conference paper (Refereed)
    Abstract [en]

    Nek5000 is a computational fluid dynamics code based on the spectral element method used for the simulation of incompressible flows. We follow up on an earlier study which ported the simplified version of Nek5000 to a GPU-accelerated system by presenting the hybrid CPU/GPU implementation of the full Nek5000 code using OpenACC. The matrix-matrix multiplication, the Nek5000 gather-scatter operator and a preconditioned Conjugate Gradient solver have implemented using OpenACC for multi-GPU systems. We report an speed-up of 1.3 on single node of a Cray XK6 when using OpenACC directives in Nek5000. On 512 nodes of the Titan supercomputer, the speed-up can be approached to 1.4. A performance analysis of the Nek5000 code using Score-P and Vampir performance monitoring tools shows that overlapping of GPU kernels with host-accelerator memory transfers would considerably increase the performance of the OpenACC version of Nek5000 code.

  • 10.
    Gong, Jing
    et al.
    Uppsala Univ, IT dept..
    Nordström, Jan
    A Stable and Efficient Hybrid Scheme for Viscous Problems in Complex Geometries2007Report (Other academic)
  • 11.
    Gong, Jing
    et al.
    Uppsala Univ., IT dept..
    Nordström, Jan
    KTH, School of Engineering Sciences (SCI), Aeronautical and Vehicle Engineering.
    A stable and efficient hybrid scheme for viscous problems in complex geometries2007In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 226, no 2, p. 1291-1309Article in journal (Refereed)
    Abstract [en]

    In this paper, we present a stable hybrid scheme for viscous problems. The hybrid method combines the unstructured finite volume method with high-order finite difference methods on complex geometries. The coupling procedure between the two numerical methods is based on energy estimates and stable interface conditions are constructed. Numerical calculations show that the hybrid method is efficient and accurate.

  • 12.
    Gong, Jing
    et al.
    Uppsala Univ., IT dept..
    Nordström, Jan
    A Stable Hybrid Method for Hyperbolic Problems2004Report (Other academic)
  • 13.
    Gong, Jing
    et al.
    Uppsala University, Sweden.
    Nordström, Jan
    Linköping University, Sweden .
    Interface procedures for finite difference approximations of the advection-diffusion equation2011In: Journal of Computational and Applied Mathematics, ISSN 0377-0427, Vol. 236, no 5, p. 602-620Article in journal (Refereed)
    Abstract [en]

    We investigate several existing interface procedures for finite difference methods applied to advection-diffusion problems. The accuracy, stiffness and reflecting properties of various interface procedures are investigated. The analysis and numerical experiments show that there are only minor differences between various methods once a proper parameter choice has been made.

  • 14.
    Gong, Jing
    et al.
    Uppsala Univ., IT dept..
    Nordström, Jan
    Stable, Accurate and Efficient Interface Procedures for Viscous Problems2006Report (Other academic)
  • 15.
    Gong, Jing
    et al.
    Uppsala Univ., IT dept..
    Nordström, Jan
    van der Weide, Edwin
    A Hybrid Method for the Unsteady Compressible Navier-Stokes Equations2007Report (Other academic)
  • 16.
    Gong, Jing
    et al.
    Uppsala Univ., IT dept..
    Svärd, Magnus
    Nordström, Jan
    Artificial Dissipation for Strictly Stable Finite Volume Methods on Unstructured Meshes2004In: Computational Mechanics Abstracts: Volume II, 2004, p. 7-7Conference paper (Refereed)
  • 17.
    Hess, Berk
    et al.
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Pall, Szilard
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Peplinski, Adam
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control.
    Highly Tuned Small Matrix Multiplications Applied to Spectral Element Code Nek50002016Conference paper (Refereed)
  • 18.
    Ivanov, Ilya
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC.
    Akhmetova, Dana
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Peng, Ivy Bo
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Machado, Rui
    Rahn, Mirko
    Bartsch, Valeria
    Hart, Alistair
    Fischer, Paul
    Evaluation of Parallel Communication Models in Nekbone, a Nek5000 mini-application2015In: 2015 IEEE International Conference on Cluster Computing, IEEE , 2015, p. 760-767Conference paper (Refereed)
    Abstract [en]

    Nekbone is a proxy application of Nek5000, a scalable Computational Fluid Dynamics (CFD) code used for modelling incompressible flows. The Nekbone mini-application is used by several international co-design centers to explore new concepts in computer science and to evaluate their performance. We present the design and implementation of a new communication kernel in the Nekbone mini-application with the goal of studying the performance of different parallel communication models. First, a new MPI blocking communication kernel has been developed to solve Nekbone problems in a three-dimensional Cartesian mesh and process topology. The new MPI implementation delivers a 13% performance improvement compared to the original implementation. The new MPI communication kernel consists of approximately 500 lines of code against the original 7,000 lines of code, allowing experimentation with new approaches in Nekbone parallel communication. Second, the MPI blocking communication in the new kernel was changed to the MPI non-blocking communication. Third, we developed a new Partitioned Global Address Space (PGAS) communication kernel, based on the GPI-2 library. This approach reduces the synchronization among neighbor processes and is on average 3% faster than the new MPI-based, non-blocking, approach. In our tests on 8,192 processes, the GPI-2 communication kernel is 3% faster than the new MPI non-blocking communication kernel. In addition, we have used the OpenMP in all the versions of the new communication kernel. Finally, we highlight the future steps for using the new communication kernel in the parent application Nek5000.

  • 19.
    Ivanov, Ilya
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Machado, Rui
    Rahn, Mirko
    Akhmetova, Dana
    KTH, School of Computer Science and Communication (CSC), Computational Science and Technology (CST).
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Henningson, Dan
    KTH, School of Engineering Sciences (SCI), Mechanics, Stability, Transition and Control. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fischer, Paul
    Markidis, Stefano
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Evaluating New Communication Models in the Nek5000 Code for Exascale2015Conference paper (Other academic)
  • 20.
    Markidis, Stefano
    et al.
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Gong, Jing
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz).
    Schliephake, Michael
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Laure, Erwin
    KTH, School of Computer Science and Communication (CSC), High Performance Computing and Visualization (HPCViz). KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Hart, Alistair
    Henty, David
    Heisey, Katherine
    Fischer, Paul
    OpenACC acceleration of the Nek5000 spectral element code2015In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 29, no 3, p. 311-319Article in journal (Refereed)
    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.

  • 21. Nordström, Jan
    et al.
    Eriksson, Sofia
    Law, Craig
    Gong, Jing
    Uppsala Univ., IT dept..
    Shock and vortex calculations using a very high order accurate Euler and Navier-Stokes solver2009In: Journal of Mechanics and MEMS, ISSN 0974-8407, Vol. 1, no 1, p. 19-26Article in journal (Refereed)
  • 22. Nordström, Jan
    et al.
    Gong, Jing
    Uppsala Univ., IT dept..
    A Stable and Efficient Hybrid Method for Aeroacoustic Sound Generation and Propagation2003In: Proc. Computational Aeroacoustics: From acoustic sources modeling to far-field radiated noise prediction, 2003Conference paper (Refereed)
  • 23. Nordström, Jan
    et al.
    Gong, Jing
    Uppsala Univ., IT dept..
    A stable and efficient hybrid method for aeroacoustic sound generation and propagation2005In: Comptes rendus. Mecanique, ISSN 1631-0721, E-ISSN 1873-7234, Vol. 333, no 9, p. 713-718Article in journal (Refereed)
    Abstract [en]

    We discuss how to combine the node based unstructured finite volume method widely used to handle complex geometries and nonlinear phenomena with very efficient high order finite difference methods suitable for wave propagation dominated problems. This fully coupled numerical procedure reflects the coupled character of the sound generation and propagation problem. The coupling procedure is based on energy estimates and stability can be guaranteed. Numerical experiments using finite difference methods that shed light on the theoretical results are performed. To cite this article: J. Nordstrom, J. Gong, C R. Mecanique 333 (2005).

  • 24. Nordström, Jan
    et al.
    Gong, Jing
    Uppsala Univ..
    A stable hybrid method for hyperbolic problems2006In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 212, no 2, p. 436-453Article in journal (Refereed)
    Abstract [en]

    A stable hybrid method for hyperbolic problems that combines the unstructured finite volume method with high-order finite difference methods has been developed. The coupling procedure is based on energy estimates and stability can be guaranteed. Numerical calculations verify that the hybrid method is efficient and accurate.

  • 25. Nordström, Jan
    et al.
    Gong, Jing
    Uppsala Univ., IT dept..
    van der Weide, Edwin
    Svärd, Magnus
    A stable and conservative high order multi-block method for the compressible Navier-Stokes equations2009Report (Other academic)
  • 26. Nordström, Jan
    et al.
    Gong, Jing
    Uppsala Univ., IT dept..
    van der Weide, Edwin
    Svärd, Magnus
    A stable and conservative high order multi-block method for the compressible Navier-Stokes equations2009In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 228, no 24, p. 9020-9035Article in journal (Refereed)
    Abstract [en]

    A stable and conservative high order multi-block method for the time-dependent compressible Navier-Stokes equations has been developed. Stability and conservation are proved using summation-by-parts operators, weak interface conditions and the energy method. This development makes it possible to exploit the efficiency of the high order finite difference method for non-trivial geometries. The computational results corroborate the theoretical analysis.

  • 27. Nordström, Jan
    et al.
    Ham, Frank
    Shoeybi, Mohammad
    van der Weide, Edwin
    Svärd, Magnus
    Mattsson, Ken
    Iaccarino, Gianluca
    Gong, Jing
    Department of Information Technology, Scientific Computing, Uppsala University.
    A Hybrid Method for Unsteady Fluid Flow2007Report (Other academic)
    Abstract [en]

    We show how a stable and accurate hybrid procedure for fluid flow can be constructed.Two separate solvers, one using high order finite difference methods andanother using the node-centered unstructured finite volume method are coupled ina truly stable way. The two flow solvers run independently and receive and sendinformation from each other by using a third coupling code. Exact solutions to theEuler equations are used to verify the accuracy and stability of the new computationalprocedure. We also demonstrate the capability of the new procedure in acalculation of the flow in and around a model of a coral.

  • 28. Nordström, Jan
    et al.
    Ham, Frank
    Shoeybi, Mohammad
    van der Weide, Edwin
    Svärd, Magnus
    Mattsson, Ken
    Laccarino, Gianluca
    Gong, Jing
    Uppsala Univ., IT dept..
    A hybrid method for unsteady inviscid fluid flow2009In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 38, no 4, p. 875-882Article in journal (Refereed)
    Abstract [en]

    We show how a stable and accurate hybrid procedure for fluid flow can be constructed. Two separate solvers, one using high order finite difference methods and another using the node-centered unstructured finite volume method are coupled in a truly stable way. The two flow solvers run independently and receive and send information from each other by using a third coupling code. Exact solutions to the Euler equations are used to verify the accuracy and stability of the new computational procedure. We also demonstrate the capability of the new procedure in a calculation of the flow in and around a model of a coral.

  • 29.
    Offermans, Nicolas
    et al.
    KTH, School of Engineering Sciences (SCI), Mechanics. KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW.
    Marin, O.
    Schanen, M.
    Gong, Jing
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Fischer, P.
    Schlatter, Philipp
    KTH, School of Engineering Sciences (SCI), Centres, Linné Flow Center, FLOW. KTH, School of Engineering Sciences (SCI), Mechanics.
    On the strong scaling of the spectral element solver Nek5000 on petascale systems2016In: Proceedings of the 2016 Exascale Applications and Software Conference (EASC2016): April 25-29 2016, Stockholm, Sweden, Association for Computing Machinery (ACM), 2016, article id a5Conference paper (Refereed)
    Abstract [en]

    The present work is targeted at performing a strong scaling study of the high-order spectral element uid dynamics solver Nek5000. Prior studies such as [5] indicated a recommendable metric for strong scalability from a theoretical viewpoint, which we test here extensively on three parallel machines with different performance characteristics and interconnect networks, namely Mira (IBM Blue Gene/Q), Beskow (Cray XC40) and Titan (Cray XK7). The test cases considered for the simulations correspond to a turbulent ow in a straight pipe at four different friction Reynolds numbers Reτ = 180, 360, 550 and 1000. Considering the linear model for parallel communication we quantify the machine characteristics in order to better assess the scaling behaviors of the code. Subsequently sampling and profiling tools are used to measure the computation and communication times over a large range of compute cores. We also study the effect of the two coarse grid solvers XXT and AMG on the computational time. Super-linear scaling due to a reduction in cache misses is observed on each computer. The strong scaling limit is attained for roughly 5000 - 10; 000 degrees of freedom per core on Mira, 30; 000 - 50; 0000 on Beskow, with only a small impact of the problem size for both machines, and ranges between 10; 000 and 220; 000 depending on the problem size on Titan. This work aims at being a reference for Nek5000 users and also serves as a basis for potential issues to address as the community heads towards exascale supercomputers.

  • 30. Otten, Matthew
    et al.
    Gong, Jing
    KTH, School of Computer Science and Communication (CSC), Centres, Centre for High Performance Computing, PDC. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Mametjanov, Azamat
    Vose, Aaron
    Levesque, John
    Fischer, Paul
    Min, Misun
    An MPI/OpenACC implementation of a high-order electromagnetics solver with GPUDirect communication2016In: The international journal of high performance computing applications, ISSN 1094-3420, E-ISSN 1741-2846, Vol. 30, no 3, p. 320-334Article in journal (Refereed)
    Abstract [en]

    We present performance results and an analysis of a message passing interface (MPI)/OpenACC implementation of an electromagnetic solver based on a spectral-element discontinuous Galerkin discretization of the time-dependent Maxwell equations. The OpenACC implementation covers all solution routines, including a highly tuned element-by-element operator evaluation and a GPUDirect gather-scatter kernel to effect nearest neighbor flux exchanges. Modifications are designed to make effective use of vectorization, streaming, and data management. Performance results using up to 16,384 graphics processing units of the Cray XK7 supercomputer Titan show more than 2.5x speedup over central processing unit-only performance on the same number of nodes (262,144 MPI ranks) for problem sizes of up to 6.9 billion grid points. We discuss performance-enhancement strategies and the overall potential of GPU-based computing for this class of problems.

  • 31. Svärd, Magnus
    et al.
    Gong, Jing
    Uppsala Univ., IT dept..
    Nordstroem, Jan
    An accuracy evaluation of unstructured node-centred finite volume methods2008In: Applied Numerical Mathematics, ISSN 0168-9274, E-ISSN 1873-5460, Vol. 58, no 8, p. 1142-1158Article in journal (Refereed)
    Abstract [en]

    Node-centred edge-based finite volume approximations are very common in computational fluid dynamics since they are assumed to run on structured, unstructured and even on mixed grids. We analyse the accuracy properties of both first and second derivative approximations and conclude that these schemes cannot be used on arbitrary grids as is often assumed. For the Euler equations first-order accuracy can be obtained if care is taken when constructing the grid. For the Navier-Stokes equations, the grid restrictions are so severe that these finite volume schemes have little advantage over structured finite difference schemes. Our theoretical results are verified through extensive computations.

  • 32. Svärd, Magnus
    et al.
    Gong, Jing
    Uppsala Univ., IT dept..
    Nordstrom, Jan
    Stable artificial dissipation operators for finite volume schemes on unstructured grids2006In: Applied Numerical Mathematics, ISSN 0168-9274, E-ISSN 1873-5460, Vol. 56, no 12, p. 1481-1490Article in journal (Refereed)
    Abstract [en]

    Our objective is to derive stable first-, second- and fourth-order artificial dissipation operators for node based finite volume schemes. Of particular interest are general unstructured grids where the strength of the finite volume method is fully utilised. A commonly used finite volume approximation of the Laplacian will be the basis in the construction of the artificial dissipation. Both a homogeneous dissipation acting in all directions with equal strength and a modification that allows different amount of dissipation in different directions are derived. Stability and accuracy of the new operators are proved and the theoretical results are supported by numerical computations.

  • 33. Svärd, Magnus
    et al.
    Gong, Jing
    Uppsala Univ., IT dept..
    Nordström, Jan
    An Accuracy Evaluation of Unstructured Node-Centred Finite Volume Methods2005Report (Other academic)
  • 34. Svärd, Magnus
    et al.
    Gong, Jing
    Uppsala Univ., IT dept..
    Nordström, Jan
    Stable Artificial Dissipation Operators for Finite Volume Schemes on Unstructured Grids2005Report (Other academic)
1 - 34 of 34
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