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7th European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS Congress 2016

作者： Krishnasamy, Ezhilmathi Hoffman, Johan Jansson, Johan BCAM - Basque Center for Applied Mathematics Mazarredo 14 Bilbao48009 Spain Department of High Performance Computing and Visualization KTH Royal Institute of Technology StockholmSE-10044 Sweden

ISBN: (纸本)9786188284401

high-Reynolds number turbulent incompressible multiphase flow represents a large class of engineering problems of key relevance to society. Here we describe our work on modeling two such problems: 1. The Consorcio de Aguas Bilbao Bizkaia is constructing a new storm tank system with an automatic cleaning system, based on periodically pushing tank water out in a tunnel 2. In the framework of the collaboration between BCAM - Basque Center for Applied Mathematics and Tecnalia R & I, the interaction of the sea flow with a semi submersible floating offshore wind platform is computationally investigated. We study the MARIA' benchmark modeling breaking waves over objects in marine environments. Both of these problems are modeled in the the Direct FEM/General Galerkin methodology for turbulent incompressible variable-densitv flow 1,2 in the FEniCS software framework.

关键词： Reynolds number

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Development of a Training Framework for Novel Accelerators 53

Development of a Training Framework for Novel Accelerators

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53rd IEEE ASEE Frontiers in Education International Conference, FIE 2023

作者： He, Zhenhua Nite, Sandra Winchell, Joshua Nasari, Abhinand Le, Hieu Tao, Jiao Chakravorty, Dhruva Perez, Lisa Liu, Honggao Texas A&m University High Performance Research Computing College StationTX United States Texas A&m University Department of Electrical and Computer Engineering College StationTX United States Texas A&m University Department of Visualization College StationTX United States

ISBN: (纸本)9798350336429

In recent years, accelerators such as Graphics Processing Units (GPUs), Field Programmable Gate Arrays (FPGAs), and Intelligence Processing Units (IPUs) have played a dominant role in speeding up workflows in science and engineering. They provide significant increases in computing power, but scientists need to learn how to effectively use these accelerators. To assist researchers, a training framework, called 'Technology Laboratories', was developed. The Technology Laboratories approach builds on situated learning and constructivism by introducing researchers to new computing concepts by scaffolding with existing knowledge of computing resources like GPUs and Jupyter Notebooks. In this approach, researchers are introduced to the newer computing methods by employing accelerators and interactive technologies familiar to them. The first iteration of the training framework was used to teach researchers how to use different methods of artificial intelligence and machine learning (AI/ML) through exercises built on familiar computing environments. New accelerator technologies like IPUs have focused on employing these AI/ML techniques, presenting an opportunity to now teach new computing accelerators using AI/ML models as the familiar computing method. Lave and Wenger's model of situated learning through a community of practice is appropriate for this learning. Additionally, Jerome Bruner's constructivist theory is part of the model as researchers are also required to construct their own knowledge about transforming their code and learning to adapt to a new type of hardware as they work through the individual characteristics of their code and research area. In this paper, we demonstrate the success of our training framework in using AI/ML methods to teach researchers about IPUs. We attracted interested participants from all over the United States, and they were able to complete hands-on exercises and run code on IPUs. We also had in-depth discussions with participants about

关键词： AI/ML Intelligence Processing Units Novel Accelerators Training Framework

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Visual MPI performance Analysis using Event Flow Graphs

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Procedia Computer Science 2015年 51卷 1353-1362页

作者： Xavier Aguilar Karl Fürlinger Erwin Laure KTH Royal Institute of Technology High Performance Computing and Visualization Department (HPCViz) and Swedish e-Science Research Center (SeRC) Ludwig-Maximilians-Universität (LMU) Munich Computer Science Department MNM Team

Event flow graphs used in the context of performance monitoring combine the scalability and low overhead of profiling methods with lossless information recording of tracing tools. In other words, they capture statistics on the performance behavior of parallel applications while pre- serving the temporal ordering of events. Event flow graphs require significantly less storage than regular event traces and can still be used to recover the full ordered sequence of events performed by the application. In this paper we explore the usage of event flow graphs in the context of visual performance analysis. We show that graphs can be used to quickly spot performance problems, helping to better understand the behavior of an application. We demonstrate our performance analysis approach with MiniFE, a mini-application that mimics the key performance aspects of finite- element applications in high performance computing (HPC).

关键词： visual performance analysis event flow graphs loop detection MPI monitoring

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Online performance Data Introspection with IPM

Online Performance Data Introspection with IPM

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IEEE International Conference on high performance computing and Communications (HPCC)

作者： Xavier Aguilar Erwin Laure Karl Fürlinger High Performance Computing and Visualization Department (HPCViz) KTH Royal Institute of Technology Stockholm Sweden Munich Computer Science Department Ludwig-Maximilians-Universität (LMU) Munich Germany

Exascale systems will be heterogeneous architectures with multiple levels of concurrency and energy constraints. In such a complex scenario, performance monitoring and runtime systems play a major role to obtain good application performance and scalability. Furthermore, online access to performance data becomes a necessity to decide how to schedule resources and orchestrate computational elements: processes, threads, tasks, etc. We present the performance Introspection API, an extension of the IPM tool that provides online runtime access to performance data from an application while it runs. We describe its design and implementation and show its overhead on several test benchmarks. We also present a real test case using the performance Introspection API in conjunction with processor frequency scaling to reduce power consumption.

关键词： Runtime Power demand Benchmark testing Clocks Monitoring Hardware performance analysis

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Patient-specific flow simulation of the left ventricle from 4D echocardiography - feasibility and robustness evaluation

Patient-specific flow simulation of the left ventricle from ...

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IEEE Symposium (IUS) Ultrasonics

作者： David Larsson Jeannette H Spühler Tim Nordenfur Johan Hoffmany Massimiliano Colarieti-Tosti Hang Gao Matilda Larsson Department of Medical Engineering KTH Royal Institute of Technology Huddinge Sweden Department of High Performance Computing and Visualization KTH Royal Institute of Technology Stockholm Sweden Department of High Performance Computing and Visualization KTH Royal Institute of Technology Lindstedtsvägen 5 SE-10044 Stockholm Sweden Department of Medical Engineering KTH Royal Institute of Technology Alfred Nobels Allé 10 SE-14152 Huddinge Sweden Lab on Cardiovascular Imaging and Dynamics Leuven Belgium

ISBN: (纸本)9781479981830

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.

关键词： Pathology Computational modeling Computational fluid dynamics Heart Robustness Doppler effect Mathematical model

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high performance Solvers for Implicit Particle in Cell Simulation

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Procedia Computer Science 2013年 18卷 2251-2258页

作者： Pawan Kumar Stefano Markidis Giovanni Lapenta Karl Meerbergen Dirk Roose Department of Computer Science Celestijnenlaan 200A 3001 Heverlee Belgium Flanders Exascience Lab (Intel Labs Europe) Heverlee Belgium High Performance Computing and Visualization (HPCViz) Department KTH Royal Institute of Technology Stockholm Sweden Center for Plasma Astrophysics Department of Mathematics Celestijnenlaan 200B Heverlee Belgium

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 magnetohy- drodynamics 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.

关键词： Implicit PIC Algebraic multigrid Krylov solvers Distributed memory

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Energetics of Kinetic Reconnection in a Three-Dimensional Null-Point Cluster

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Physical Review Letters 2013年第4期111卷 045002-045002页

作者： V. Olshevsky G. Lapenta S. Markidis Center for mathematical Plasma Astrophysics (CmPA) Department of Mathematics KU Leuven Celestijnenlaan 200B bus 2400 B-3001 Leuven Belgium Main Astronomical Observatory of NAS Akademika Zabolotnoho 27 03680 Kyiv Ukraine High Performance Computing and Visualization (HPCViz) KTH Royal Institute of Technology SE-100 44 Stockholm Sweden

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.

关键词： ION beams KINETIC energy MAGNETIC reconnection MAGNETIC field effects SYMMETRIES (Quantum mechanics)

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Development of a Training Framework for Novel Accelerators

Development of a Training Framework for Novel Accelerators

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Frontiers in Education (FIE) Conference

作者： Zhenhua He Sandra Nite Joshua Winchell Abhinand Nasari Hieu Le Jiao Tao Dhruva Chakravorty Lisa Perez Honggao Liu High Performance Research Computing Texas A&M University College Station TX USA Department of Electrical and Computer Engineering Texas A&M University College Station TX USA Department of Visualization Texas A&M University College Station TX USA

In recent years, accelerators such as Graphics Processing Units (GPUs), Field Programmable Gate Arrays (FPGAs), and Intelligence Processing Units (IPUs) have played a dominant role in speeding up workflows in science and engineering. They provide significant increases in computing power, but scientists need to learn how to effectively use these accelerators. To assist researchers, a training framework, called “Technology Laboratories”, was developed. The Technology Laboratories approach builds on situated learning and constructivism by introducing researchers to new computing concepts by scaffolding with existing knowledge of computing resources like GPUs and Jupyter Notebooks. In this approach, researchers are introduced to the newer computing methods by employing accelerators and interactive technologies familiar to them. The first iteration of the training framework was used to teach researchers how to use different methods of artificial intelligence and machine learning (AI/ML) through exercises built on familiar computing environments. New accelerator technologies like IPUs have focused on employing these AI/ML techniques, presenting an opportunity to now teach new computing accelerators using AI/ML models as the familiar computing method. Lave and Wenger's model of situated learning through a community of practice is appropriate for this learning. Additionally, Jerome Bruner's constructivist theory is part of the model as researchers are also required to construct their own knowledge about transforming their code and learning to adapt to a new type of hardware as they work through the individual characteristics of their code and research area. In this paper, we demonstrate the success of our training framework in using AI/ML methods to teach researchers about IPUs. We attracted interested participants from all over the United States, and they were able to complete hands-on exercises and run code on IPUs. We also had in-depth discussions with participants about

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Electromagnetic Particle-in-Cell Simulations of the Solar Wind Interaction with Lunar Magnetic Anomalies

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Physical Review Letters 2014年第15期112卷 151102-151102页

作者： J. Deca A. Divin G. Lapenta B. Lembège S. Markidis M. Horányi Centre for mathematical Plasma Astrophysics (CmPA) Department of Mathematics KU Leuven Celestijnenlaan 200B bus 2400 B-3001 Leuven Belgium Laboratoire Atmosphères Milieux Observations Spatiales (LATMOS) Université de Versailles à Saint Quentin 11 Boulevard D’Alembert 78280 Guyancourt France Swedish Institute of Space Physics (IRF) SE-751 21 Uppsala Sweden High Performance Computing and Visualization (HPCViz) KTH Royal Institute of Technology SE-100 44 Stockholm Sweden Laboratory for Atmospheric and Space Physics (LASP) University of Colorado 1234 Innovation Drive Boulder Colorado 80303-7814 USA

We present the first three-dimensional fully kinetic and electromagnetic simulations of the solar wind interaction with lunar crustal magnetic anomalies (LMAs). Using the implicit particle-in-cell code iPic3D, we confirm that LMAs may indeed be strong enough to stand off the solar wind from directly impacting the lunar surface forming a mini-magnetosphere, as suggested by spacecraft observations and theory. In contrast to earlier magnetohydrodynamics and hybrid simulations, the fully kinetic nature of iPic3D allows us to investigate the space charge effects and in particular the electron dynamics dominating the near-surface lunar plasma environment. We describe for the first time the interaction of a dipole model centered just below the lunar surface under plasma conditions such that only the electron population is magnetized. The fully kinetic treatment identifies electromagnetic modes that alter the magnetic field at scales determined by the electron physics. Driven by strong pressure anisotropies, the mini-magnetosphere is unstable over time, leading to only temporal shielding of the surface underneath. Future human exploration as well as lunar science in general therefore hinges on a better understanding of LMAs.

关键词： MAGNETOHYDRODYNAMICS MAGNETIC anomalies FLUID dynamics MAGNETIC field effects ELECTRONS HYBRID computer simulation

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A MULTIGRID REDUCTION FRAMEWORK FOR DOMAINS WITH SYMMETRIES

arXiv

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arXiv 2024年

作者： Alsalti-Baldellou, Àdel Janna, Carlo Álvarez-Farré, Xavier Xavier Trias, F. Department of Information Engineering University of Padova Via Giovanni Gradenigo 6b Padova PD35131 Italy Heat and Mass Transfer Technological Center Universitat Politècnica de Catalunya BarcelonaTech Carrer de Colom 11 Terrassa08222 Spain Department of Civil Environmental and Architectural Engineering University of Padova Via Francesco Marzolo 9 Padova PD35131 Italy M3E S.r.l. Via Giambellino 7 Padova PD35129 Italy High-Performance Computing and Visualization Team SURF Science Park 140 Amsterdam1098 XG Netherlands

Divergence constraints are present in the governing equations of numerous physical phenomena, and they usually lead to a Poisson equation whose solution represents a bottleneck in many simulation codes. Algebraic Multigrid (AMG) is arguably the most powerful preconditioner for Poisson’s equation, and its effectiveness results from the complementary roles played by the smoother, responsible for damping high-frequency error components, and the coarse-grid correction, which in turn reduces low-frequency modes. This work presents several strategies to make AMG more compute-intensive by leveraging reflection, translational and rotational symmetries. AMGR, our final proposal, does not require boundary conditions to be symmetric, therefore applying to a broad range of academic and industrial configurations. It is based on a multigrid reduction framework that introduces an aggressive coarsening to the multigrid hierarchy, reducing the memory footprint, setup and application costs of the top-level smoother. While preserving AMG’s excellent convergence, AMGR allows replacing the standard sparse matrix-vector product with the more compute-intensive sparse matrix-matrix product, yielding significant accelerations. Numerical experiments on industrial CFD applications demonstrated up to 70% speed-ups when solving Poisson’s equation with AMGR instead of AMG. Additionally, strong and weak scalability analyses revealed no significant *** Codes 65F08, 65F50, 65N55, 65Y05 © 2024, CC BY-NC-ND.

关键词： Poisson equation

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