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A domain-specific language and matrix-free stencil code for investigating electronic properties of Dirac and topological materials

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INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 2021年第1期35卷 60-77页

作者： Pieper, Andreas Hager, Georg Fehske, Holger Ernst Moritz Arndt Univ Greifswald Phys Greifswald Germany Friedrich Alexander Univ Erlangen Nurnberg Erlangen Reg Comp Ctr RRZE Martensstr 1 D-91058 Erlangen Germany

We introduce PVSC-DTM (Parallel Vectorized stencil code for Dirac and Topological Materials), a library and code generator based on a domain-specific language tailored to implement the specific stencil-like algorithms that can describe Dirac and topological materials such as graphene and topological insulators in a matrix-free way. The generated hybrid-parallel (MPI+OpenMP) code is fully vectorized using Single Instruction Multiple Data (SIMD) extensions. It is significantly faster than matrix-based approaches on the node level and performs in accordance with the roofline model. We demonstrate the chip-level performance and distributed-memory scalability of basic building blocks such as sparse matrix-(multiple-) vector multiplication on modern multicore CPUs. As an application example, we use the PVSC-DTM scheme to (i) explore the scattering of a Dirac wave on an array of gate-defined quantum dots, to (ii) calculate a bunch of interior eigenvalues for strong topological insulators, and to (iii) discuss the photoemission spectra of a disordered Weyl semimetal.

关键词： stencil code domain-specific language topological quantum matter

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Massively Parallel stencil code Solver with Autonomous Adaptive Block Distribution

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IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 2018年第10期29卷 2282-2296页

作者： Berghoff, Marco Kondov, Ivan Hoetzer, Johannes KIT SCC Hermann von Helmholtz Pl 1 D-76344 Eggenstein Leopoldshafen Germany KIT IAM Str Forum 7 D-76131 Karlsruhe Germany Karlsruhe Univ Appl Sci Inst Mat & Proc Moltkestr 30 D-76133 Karlsruhe Germany

In the last decades, simulations have been established in several fields of science and industry to study various phenomena by solving, inter alia, partial differential equations. For an efficient use of current and future high performance computing systems, with many thousands of computation ranks, high node-level performance, scalable communication, and the omission of unnecessary calculations are of high priority in the development of new solvers. The challenge of contemporary simulation applications is to bridge the gap between the scales of the various physical processes. We introduce the NAStJA framework, a block-based MPI parallel solver for arbitrary algorithms, based on stencil code or other regular grid methods. NAStJA decomposes the domain of spatially complex structures into small cuboid blocks. A special feature of NAStJA is the dynamic block adaption which modifies the calculation domain around the region where the computation currently takes place, and hence avoids unnecessary calculations. This often occurs, inter alia, in phase-field simulations. Block creation and deletion is managed autonomously within local neighborhoods. A basic load balancing mechanism allows a re-distribution of newly created blocks to the involved computing ranks. The use of a multi-hop network, to distribute information to the entire domain, avoids collective all-gather communications. Thus, we can demonstrate excellent scaling. The present scaling tests substantiate the enormous advantage of this adaptive method. For certain simulation scenarios, we can show that the calculation effort and memory consumption can be reduced to only 3.5 percent, compared to the classical full-domain reference simulation. The overhead of 70-100 percent for the dynamic adapting block creation is significantly lower than the gain. The approach is not restricted to phase-field simulations, and can be employed in other domains of computational science to exploit sparsity of computing regions.

关键词： stencil code distributed memory scalable parallel algorithms massively parallel performance multi-hop network load balancing partial differential equation phase-field method

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On GPU optimizations of stencil codes for highly parallel simulations 29

On GPU optimizations of stencil codes for highly parallel si...

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29th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP)

作者： Pfisterer, Nikolai Berghoff, Marco Streit, Achim Karlsruhe Inst Technol Steinbuch Ctr Comp Karlsruhe Germany

ISBN: (纸本)9781665414555

stencil codes are valuable methods to solve partial differential equations of models in a wide range of applications in science and engineering. Graphics processing units (GPUs) provide a highly parallel architecture with fast directly accessible memory that is desirable to run stencil codes. They enable larger and more complex simulations that are solved faster compared to simulating on CPUs. We provide a solution for users to run highly parallel stencil codes on GPUs, that can also be efficiently used on a distributed GPU cluster. In this work, we present an extension to the multi-disciplinary framework NAStJA originally designed to efficiently run stencil codes on the CPUs in current high-performance computing (HPC) systems, to also be able to run on GPUs. We describe different methods to increase the performance of stencil codes on GPUs like a border exchange method which is transparent to the user, as well as a buffer for gradient values that are needed multiple times. We show their performance using the phase-field method as a stencil code example. With this GPU extension and optimizations implemented into the NAStJA framework, we can show highly improved performance compared to the CPU implementation, and an efficiency of 92% (weak scaling) for a large-scale example simulation on 64 GPUs on the ForHLR II HPC system.

关键词： GPU optimizations stencil code heterogeneous parallelization scalability analysis scalability analysis

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Automatic Acceleration of stencil codes in Android Devices 17th

Automatic Acceleration of Stencil Codes in Android Devices

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17th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP)

作者： Afonso, Ergio Acosta, Alejandro Almeida, Francisco Univ La Laguna San Cristobal De La Lagu Spain

ISBN: (纸本)9783319654829;9783319654812

The increase of performance in handheld devices due to their widespread adoption has required the integration of several distinct kinds of processor in a single chip. These technologies have turned current Systems on Chip into heterogeneous platforms. stencil codes are a family of algorithms that appear in many relevant scientific and image processing codes. In order to improve the performance of these algorithms in heterogeneous platforms, the usage of accelerators is very important but, for a mobile applications developer, the development cost is very high. We propose a methodology, based in our framework Paralldroid, for automatically generating accelerated implementations of several well-known representative stencil codes. The performance of these codes has also been measured in order to demonstrate how Paralldroid is able to accelerate code without extensive or complex modifications. Results show great performance improvements for few code modifications.

关键词： Android OpenCL stencil code Source-to-source translation Parallelizing compiler Renderscript

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Massively Parallel stencil Strategies for Radiation Transport Moment Model Simulations 20th

Massively Parallel Stencil Strategies for Radiation Transpor...

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20th Annual International Conference on Computational Science (ICCS)

作者： Berghoff, Marco Frank, Martin Seibold, Benjamin Karlsruhe Inst Technol Steinbuch Ctr Comp Karlsruhe Germany Temple Univ Dept Math Philadelphia PA 19122 USA

ISBN: (纸本)9783030504366;9783030504359

The radiation transport equation is a mesoscopic equation in high dimensional phase space. Moment methods approximate it via a system of partial differential equations in traditional space-time. One challenge is the high computational intensity due to large vector sizes (1 600 components for P39) in each spatial grid point. In this work, we extend the calculable domain size in 3D simulations considerably, by implementing the StaRMAP methodology within the massively parallel HPC framework NAStJA, which is designed to use current supercomputers efficiently. We apply several optimization techniques, including a new memory layout and explicit SIMD vectorization. We showcase a simulation with 200 billion degrees of freedom, and argue how the implementations can be extended and used in many scientific domains.

关键词： Radiation transport Moment methods stencil code Massively parallel

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A PGAS Execution Model for Efficient stencil Computation on Many-Core Processors 14

A PGAS Execution Model for Efficient Stencil Computation on ...

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14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)

作者： Ikei, Mitsuru Sato, Mitsuhisa Univ Tsukuba Dept Comp Sci Intel KK Intel Architecture Technol Grp Tokyo Japan Univ Tsukuba Dept Comp Sci Tsukuba Ibaraki Japan

ISBN: (纸本)9781479927845

A efficient PGAS execution model on many-core processor for stencil computation is proposed and implemented. We use XcalableMP as a base language and we modify its runtime well fit in many-core processors. The runtime uses processes for parallel execution and global arrays of the stencil codes are broken into blocked sub-arrays placed on shared memory. Using two stencil codes, Laplace and Himeno, we evaluated its performance. In the evaluation, we show (1) Blocking improves locality of memory access during computation therefore improves total CPU execution time. (2) Direct data access using shared memory can relieve communication burden of sub-array halo exchanges.

关键词： many integrated core parallel PGAS stencil code

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Automatic Adaptive Approximation for stencil Computations 2019

Automatic Adaptive Approximation for Stencil Computations

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28th International Conference on Compiler Construction (CC)

作者： Schmitt, Maxime Helluy, Philippe Bastoul, Cedric Univ Strasbourg Inria Strasbourg France

ISBN: (纸本)9781450362771

Approximate computing is necessary to meet deadlines in some compute-intensive applications like simulation. Building them requires a high level of expertise from the application designers as well as a significant development effort. Some application programming interfaces greatly facilitate their conception but they still heavily rely on the developer's domain-specific knowledge and require many modifications to successfully generate an approximate version of the program. In this paper we present new techniques to semi-automatically discover relevant approximate computing parameters. We believe that superior compiler-user interaction is the key to improved productivity. After pinpointing the region of interest to optimize, the developer is guided by the compiler in making the best implementation choices. Static analysis and runtime monitoring are used to infer approximation parameter values for the application. We evaluated these techniques on multiple application kernels that support approximation and show that with the help of our method, we achieve similar performance as non-assisted, hand-tuned version while requiring minimal intervention from the user.

关键词： Approximate Computing Compilation code Optimization Application Programming Interface stencil code

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Non-collective Scalable Global Network Based on Local Communications 9

Non-collective Scalable Global Network Based on Local Commun...

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9th IEEE/ACM Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems (scalA)

作者： Berghoff, Marco Kondov, Ivan Karlsruhe Inst Technol Steinbuch Ctr Comp Karlsruhe Germany

ISBN: (纸本)9781728101767

To efficiently perform collective communications in current high-performance computing systems is a time-consuming task. With future exascale systems, this communication time will be increased further. However, global information is frequently required in various physical models. By exploiting domain knowledge of the model behaviors globally needed information can be distributed more efficiently, using only peer-to-peer communication which spread the information to all processes asynchronous during multiple communication steps. In this article, we introduce a multi-hop based Manhattan Street Network (MSN) for global information exchange and show the conditions under which a local neighbor exchange is sufficient for exchanging distributed information. Besides the MSN, in various models, global information is only needed in a spatially limited region inside the simulation domain. Therefore, a second network is introduced, the local exchange network, to exploit this spatial assumption. Both non-collective global exchange networks are implemented in the massively parallel NAStJA framework. Based on two models, a phase-field model for droplet simulations and the cellular Potts model for biological tissue simulations, we exemplary demonstrate the wide applicability of these networks. Scaling tests of the networks demonstrate a nearly ideal scaling behavior with an efficiency of over 90%. Theoretical prediction of the communication time on future exascale systems shows an enormous advantage of the presented exchange methods of O(1) by exploiting the domain knowledge.

关键词： peer-to-peer communication distributed memory scalable parallel algorithms massive-parallel performance network protocol stencil code phase-field method

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Evaluating the OpenACC API for Parallelization of CFD Applications

Evaluating the OpenACC API for Parallelization of CFD Applic...

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作者： Pickering, Brent Phillip Virginia Tech | University

Directive-based programming of graphics processing units (GPUs) has recently appeared as a viable alternative to using specialized low-level languages such as CUDA C and OpenCL for general-purpose GPU programming. This technique, which uses directive or pragma statements to annotate source codes written in traditional high-level languages, is designed to permit a unified code base to serve multiple computational platforms and to simplify the transition of legacy codes to new architectures. This work analyzes the popular OpenACC programming standard, as implemented by the PGI compiler suite, in order to evaluate its utility and performance potential in computational fluid dynamics (CFD) applications. Of particular interest is the handling of stencil algorithms, which are an important component of finite-difference and finite-volume numerical methods. To this end, the process of applying the OpenACC Fortran API to a preexisting finite-difference CFD code is examined in detail, and all modifications that must be made to the original source in order to run efficiently on the GPU are noted. Optimization techniques for OpenACC are also explored, and it is demonstrated that tuning the code for a particular accelerator architecture can result in performance increases of over 30%. There are also some limitations and programming restrictions imposed by the API: it is observed that certain useful features of modern Fortran (2003/8) are effectively disabled within OpenACC regions. Finally, a combination of OpenACC and OpenMP directives is used to create a truly cross-platform Fortran code that can be compiled for either CPU or GPU hardware. The performance of the OpenACC code is measured on several contemporary NVIDIA GPU architectures, and a comparison is made between double and single precision arithmetic showing that if reduced precision can be tolerated, it can lead to significant speedups. To assess the performance gains relative to a typical CPU implementation, the

关键词： graphics processing unit (GPU) computational fluid dynamics (CFD) directive-based programming parallel programming OpenACC Fortran 2003 stencil code finite-volume method Thesis

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