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PittPack: An open-source Poisson's equation solver for extreme-scale computing with accelerators

COMPUTER PHYSICS COMMUNICATIONS 2020年 254卷 107272-107272页

作者： Hasbestan, Jaber J. Xiao, Cheng-Nian Senocak, Inanc Univ Pittsburgh Dept Mech Engn & Mat Sci Pittsburgh PA 15261 USA

We present a parallel implementation of a direct solver for Poisson's equation on extreme-scale supercomputers with accelerators. We introduce a chunked-pencil decomposition as the domain-decomposition strategy to distribute work among processing elements to achieve improved scalability at high counts of accelerators. Chunked-pencil decomposition enables overlapping MPI communication and data transfer between the central processing units (CPUs) and the graphics processing units (GPUs). It enables contiguous message transfer among the nodes and improves data locality by keeping neighboring elements in adjacent memory locations while permitting the use of shared memory for certain segments of the algorithm when possible. We study two different communication patterns within the chunked-pencil decomposition. The first pattern fully overlaps the communication with data transfer and aims to speedup the overall turnaround time. The second pattern concentrates on low memory usage and is more network friendly than the first pattern for computations at extreme scale. In our parallel implementation, we interleave OpenACC with MPI to support computations on the GPU or the CPU. The numerical solution and its formal second order of accuracy is verified using the method of manufactured solutions for various combinations of boundary conditions. Additionally, we used PittPack within an incompressible flow solver to further validate its accuracy and as well as demonstrate its versatility as a software package. We performed weak scaling analysis with up to 1.1 trillion Cartesian mesh points distributed over 16384 GPUs on a petascale leadership class supercomputer. Program Summary Program Title: PittPack Program Files doi: http//***/10.17632/59ktwdby4r.1 Licensing provisions: GNU General Public License 3 Programming language: C++ Nature of problem: An elliptic Poisson's equation for pressure arises in the numerical solution of incompressible fluid flow. This equation needs to be

关键词： Chunked-pencil decomposition Fast Fourier transform Parallel communication pattern Direct Poisson solver GPU computing petascale computing OpenACC

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A challenging dam structural analysis: large-scale implicit thermo-mechanical coupled contact simulation on Tianhe-II

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COMPUTATIONAL MECHANICS 2019年第1期63卷 99-119页

作者： Tian, Rong Zhou, Mozhen Wang, Jingtao Li, Yang An, Hengbin Xu, Xiaowen Wen, Longfei Wang, Lixiang Xu, Quan Leng, Juelin Xu, Ran Zhang, Bingyin Liu, Weijie Mo, Zeyao IAPCM Software Ctr High Performance Numer Simulat Beijing 100088 Peoples R China Tsinghua Univ State Key Lab Hydrosci & Engn Beijing 100084 Peoples R China

Due to huge bulk volume and extremely complex geometrical and geological features, it is forbiddingly difficult to perform a dam structural analysis with even moderate geometry fidelity in engineering practices. We present a high resolution of engineering structural analysis of the first ultra-high concrete-faced rockfill dam in China. Mesh resolution is taken to be 20cm along slab thickness for the bulk volume of 20M m3 of the whole dam. The engineering problem is solved by considering nonlinear behaviors such as joints' contact nonlinearity, creep deformation, and strong thermo-mechanical coupling, as well as blended continuous-discontinuous approximation, on a mesh model of 1.1 billion dofs using 16K CPU cores of Tianhe-II. The problem to be solved is a challenging non-positive definite, non-symmetric and ill-conditioned matrix problem. The simulation confirms in the first time that the sunlight temperature effect can contribute up to a contact stress increment of maximum 10.9 MPa and explains frequent extrusion damage observed for the dam. As model tests are difficult to perform for high dams, with this first success, we envision that extreme-scale simulation would pose broad impact on the safety evaluation of high dams in future.

关键词： petascale computing Life time safety Ultra high dams Hydraulic engineering Dual mortar method Thermo-mechanical-contact coupling Extended finite element method Preconditioning Linear solver

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Petaflop Seismic Simulations in the Public Cloud 34th

Petaflop Seismic Simulations in the Public Cloud

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34th International Conference on High Performance computing (ISC High Performance)

作者： Breuer, Alexander Cui, Yifeng Heinecke, Alexander Univ Calif San Diego La Jolla CA 92093 USA Intel Corp Santa Clara CA 95054 USA

ISBN: (纸本)9783030206567;9783030206550

During the last decade cloud services and infrastructure as a service became a popular solution for diverse applications. Additionally, hardware support for virtualization closed performance gaps, compared to on-premises, bare-metal systems. This development is driven by offloaded hypervisors and full CPU virtualization. Today's cloud service providers, such as Amazon or Google, offer the ability to assemble application-tailored clusters to maximize performance. However, from an interconnect point of view, one has to tackle a 4-5x slow-down in terms of bandwidth and 25x in terms of latency, compared to latest high-speed and low-latency interconnects. Taking into account the high per-node and accelerator-driven performance of latest supercomputers, we observe that the network-bandwidth performance of recent cloud offerings is within 2x of large supercomputers. In order to address these challenges, we present a comprehensive application-centric approach for high-order seismic simulations utilizing the ADER discontinuous Galerkin finite element method, which exhibits excellent communication characteristics. This covers the tuning of the operating system, normally not possible on supercomputers, micro-benchmarking, and finally, the efficient execution of our solver in the public cloud. Due to this performance-oriented end-to-end workflow, we were able to achieve 1.09 PFLOPS on 768 AWS c5.18xlarge instances, offering 27,648 cores with 5 PFLOPS of theoretical computational power. This correlates to an achieved peak efficiency of over 20% and a close-to 90% parallel efficiency in a weak scaling setup. In terms of strong scalability, we were able to strong-scale a science scenario from 2 to 64 instances with 60% parallel efficiency. This work is, to the best of our knowledge, the first of its kind at such a large scale.

关键词： High-order DG Seismic simulations Earthquake simulations Cloud computing petascale computing

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Large-scale large eddy simulation of nuclear reactor flows: Issues and perspectives

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NUCLEAR ENGINEERING AND DESIGN 2017年第Feb.期312卷 86-98页

作者： Merzari, Elia Obabko, Aleks Fischer, Paul Halford, Noah Walker, Justin Siegel, Andrew Yu, Yiqi Argonne Natl Lab Math & Comp Sci Div 9700 S Cass Ave Argonne IL 60439 USA Argonne Natl Lab Nucl Engn Div 9700 S Cass Ave Argonne IL 60439 USA

Numerical simulation has been an intrinsic part of nuclear engineering research since its inception. In recent years a transition is occurring toward predictive, first-principle-based tools such as computational fluid dynamics. Even with the advent of petascale computing, however, such tools still have significant limitations. In the present work some of these issues, and in particular the presence of massive multiscale separation, are discussed, as well as some of the research conducted to mitigate them. petascale simulations at high fidelity (large eddy simulation/direct numerical simulation) were conducted with the massively parallel spectral element code Nek5000 on a series of representative problems. These simulations shed light on the requirements of several types of simulation: (1) axial flow around fuel rods, with particular attention to wall effects;(2) natural convection in the primary vessel;and (3) flow in a rod bundle in the presence of spacing devices. The focus of the work presented here is on the lessons learned and the requirements to perform these simulations at exascale. Additional physical insight gained from these simulations is also emphasized. (C) 2016 Elsevier B.V. All rights reserved.

关键词： large eddy simulation petascale computing Nuclear Engineering Nuclear reactors Perspective numerical simulation

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Building a Community of Practice to Prepare the HPC Workforce

Building a Community of Practice to Prepare the HPC Workforc...

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International Conference on Computational Science (ICCS)

作者： Cahill, Katharine J. Lathrop, Scott Gordon, Steven Ohio Supercomp Ctr Columbus OH 43212 USA Shodor Educ Fdn Inc Durham NC USA

It has been well documented for more than 30 years, that significantly more effort is needed to prepare the HPC workforce needed today and well into the future. The Blue Waters Virtual School of Computational Science (VSCSE) provides an innovative model for addressing this critical need. The VSCSE uses a Small Private Online Course (SPOC) approach to providing graduate level credit courses to students at multiple institutions. In this paper, we describe the rationale for this approach, a description of the implementation, findings from external evaluations, and lessons learned. The paper concludes with recommendations for future strategies to build on this work to address the workforce needs of our global society. (C) 2017 The Authors. Published by Elsevier B.V.

关键词： HPC workforce petascale computing on-line education graduate education SPOC course

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A prospect for computing in porous materials research: Very large fluid flow simulations

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JOURNAL OF COMPUTATIONAL SCIENCE 2016年 12卷 62-76页

作者： Mattila, Keijo Puurtinen, Tuomas Hyvaluoma, Jari Surmas, Rodrigo Myllys, Markko Turpeinen, Tuomas Robertsen, Fredrik Westerholm, Jan Timonen, Jussi Univ Jyvaskyla Dept Phys POB 35 YFL FI-40014 Jyvaskyla Finland Univ Jyvaskyla Nanosci Ctr POB 35 YFL FI-40014 Jyvaskyla Finland Tampere Univ Technol Dept Phys POB 692 FI-33101 Tampere Finland Nat Resources Inst Finland Luke FI-31600 Jokioinen Finland Petrobras SA CENPES BR-21941915 Rio De Janeiro Brazil Abo Akad Univ Fac Sci & Engn Joukahainengatan 3-5 FI-20520 Turku Finland

Properties of porous materials, abundant both in nature and industry, have broad influences on societies via, e.g. oil recovery, erosion, and propagation of pollutants. The internal structure of many porous materials involves multiple scales which hinders research on the relation between structure and transport properties: typically laboratory experiments cannot distinguish contributions from individual scales while computer simulations cannot capture multiple scales due to limited capabilities. Thus the question arises how large domain sizes can in fact be simulated with modern computers. This question is here addressed using a realistic test case;it is demonstrated that current computing capabilities allow the direct pore-scale simulation of fluid flow in porous materials using system sizes far beyond what has been previously reported. The achieved system sizes allow the closing of some particular scale gaps in, e.g. soil and petroleum rock research. Specifically, a full steady-state fluid flow simulation in a porous material, represented with an unprecedented resolution for the given sample size, is reported: the simulation is executed on a CPU-based supercomputer and the 3D geometry involves 16,3843 lattice cells (around 590 billion of them are pore sites). Using half of this sample in a benchmark simulation on a GPU-based system, a sustained computational performance of 1.77 PFLOPS is observed. These advances expose new opportunities in porous materials research. The implementation techniques here utilized are standard except for the tailored high-performance data layouts as well as the indirect addressing scheme with a low memory overhead and the truly asynchronous data communication scheme in the case of CPU and GPU code versions, respectively. (c) 2015 Elsevier B.V. All rights reserved.

关键词： Porous material Permeability Fluid flow simulation Lattice Boltzmann method petascale computing GPU

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Building a Community of Practice to Prepare the HPC Workforce

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Procedia Computer Science 2017年 108卷 2131-2140页

作者： Katharine J. Cahill Scott Lathrop Steven Gordon Ohio Supercomputer Center Shodor Education Foundation Inc.

关键词： HPC workforce petascale computing on-line education graduate education SPOC course

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Towards Green Aviation with Python at petascale 16

Towards Green Aviation with Python at Petascale

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International Conference on High Performance computing, Networking, Storage and Analysis (SC)

作者： Vincent, Peter Witherden, Freddie Vermeire, Brian Park, Jin Seok Iyer, Arvind Imperial Coll London Dept Aeronaut London England

ISBN: (纸本)9781467388153

Accurate simulation of unsteady turbulent flow is critical for improved design of greener aircraft that are quieter and more fuel-efficient. We demonstrate application of PyFR, a Python based computational fluid dynamics solver, to petascale simulation of such flow problems. Rationale behind algorithmic choices, which offer increased levels of accuracy and enable sustained computation at up to 58% of peak DP-FLOP/s on unstructured grids, will be discussed in the context of modern hardware. A range of software innovations will also be detailed, including use of runtime code generation, which enables PyFR to efficiently target multiple platforms, including heterogeneous systems, via a single implementation. Finally, results will be presented from a full-scale simulation of flow over a low-pressure turbine blade cascade, along with weak/strong scaling statistics from the Piz Daint and Titan supercomputers, and performance data demonstrating sustained computation at up to 13.7 DP-PFLOP/s.

关键词： Turbines Blades Hardware Computational modeling Aircraft Aerodynamics Bandwidth petascale computing turbines Blades Aircraft Aerodynamics Computer hardware Computational modeling Pythonidae Bandwidth Python run-time code generation flow simulation design improvement HETEROGENEOUS SYSTEM unstructured grids (mathematics)

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AN EXPERIMENTAL DISTRIBUTED VISUALIZATION SYSTEM FOR petascale computing

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computing IN SCIENCE & ENGINEERING 2010年第5期12卷 78-82页

作者： Ge, Jinghua Hutanu, Andrei Toole, Cornelius Kooima, Robert Hossain, Imtiaz Allen, Gabrielle Louisiana State Univ Ctr Computat & Technol Baton Rouge LA 70803 USA Louisiana State Univ Dept Comp Sci Baton Rouge LA 70803 USA Louisiana State Univ Visualizat Serv Ctr Informat Technol Serv Baton Rouge LA 70803 USA

The coming era of petascale computing and heterogeneous platforms calls for fundamental changes in perspective on how we design distributed visualization software.

关键词： GPU cluster Scientific visualization data visualisation distributed processing distributed system distributed visualization software design experimental distributed visualization system high-speed networks petascale computing petascale computing tangible interaction.

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SPARC64 VIIIFX: A NEW-GENERATION OCTOCORE PROCESSOR FOR petascale computing

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IEEE MICRO 2010年第2期30卷 30-40页

作者： Maruyama, Takumi Yoshida, Toshio Kan, Ryuji Yamazaki, Iwao Yamamura, Shuji Takahashi, Noriyuki Hondou, Mikio Okano, Hiroshi Fujitsu Ltd Next Generat Tech Comp Unit Nakahara Ku Kawasaki Kanagawa 2118588 Japan

The Sparc64 VIIIfx eight-core processor, developed for use in petascale computing systems, runs at speeds of up to 2 GHz and achieves a peak performance of 128 gigaflops while consuming as little as 58 watts of power. Sparc64 VIIIfx realizes a six-fold improvement in performance per watt over previous generation Sparc64 processors.

关键词： hardware high performance low power multicore processor return address stack system on chip Multi-core processors LOW POWER peak performance system-on-chip petascale computing Computer hardware HIGH-PERFORMANCE PROCESSOR Energy units

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