Hardware-Oriented Krylov Methods for High-Performance Computing
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A Distributed and Parallel Asynchronous Unite and Conquer Method to Solve Large Scale Non-Hermitian Linear Systems Xinzhe Wu, Serge Petiton
A Distributed and Parallel Asynchronous Unite and Conquer Method to Solve Large Scale Non-Hermitian Linear Systems Xinzhe Wu, Serge Petiton To cite this version: Xinzhe Wu, Serge Petiton. A Distributed and Parallel Asynchronous Unite and Conquer Method to Solve Large Scale Non-Hermitian Linear Systems. HPC Asia 2018 - International Conference on High Performance Computing in Asia-Pacific Region, Jan 2018, Tokyo, Japan. 10.1145/3149457.3154481. hal-01677110 HAL Id: hal-01677110 https://hal.archives-ouvertes.fr/hal-01677110 Submitted on 8 Jan 2018 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. A Distributed and Parallel Asynchronous Unite and Conquer Method to Solve Large Scale Non-Hermitian Linear Systems Xinzhe WU Serge G. Petiton Maison de la Simulation, USR 3441 Maison de la Simulation, USR 3441 CRIStAL, UMR CNRS 9189 CRIStAL, UMR CNRS 9189 Université de Lille 1, Sciences et Technologies Université de Lille 1, Sciences et Technologies F-91191, Gif-sur-Yvette, France F-91191, Gif-sur-Yvette, France [email protected] [email protected] ABSTRACT the iteration number. These methods are already well implemented Parallel Krylov Subspace Methods are commonly used for solv- in parallel to profit from the great number of computation cores ing large-scale sparse linear systems. -
Implicitly Restarted Arnoldi/Lanczos Methods for Large Scale Eigenvalue Calculations
NASA Contractor Report 198342 /" ICASE Report No. 96-40 J ICA IMPLICITLY RESTARTED ARNOLDI/LANCZOS METHODS FOR LARGE SCALE EIGENVALUE CALCULATIONS Danny C. Sorensen NASA Contract No. NASI-19480 May 1996 Institute for Computer Applications in Science and Engineering NASA Langley Research Center Hampton, VA 23681-0001 Operated by Universities Space Research Association National Aeronautics and Space Administration Langley Research Center Hampton, Virginia 23681-0001 IMPLICITLY RESTARTED ARNOLDI/LANCZOS METHODS FOR LARGE SCALE EIGENVALUE CALCULATIONS Danny C. Sorensen 1 Department of Computational and Applied Mathematics Rice University Houston, TX 77251 sorensen@rice, edu ABSTRACT Eigenvalues and eigenfunctions of linear operators are important to many areas of ap- plied mathematics. The ability to approximate these quantities numerically is becoming increasingly important in a wide variety of applications. This increasing demand has fu- eled interest in the development of new methods and software for the numerical solution of large-scale algebraic eigenvalue problems. In turn, the existence of these new methods and software, along with the dramatically increased computational capabilities now avail- able, has enabled the solution of problems that would not even have been posed five or ten years ago. Until very recently, software for large-scale nonsymmetric problems was virtually non-existent. Fortunately, the situation is improving rapidly. The purpose of this article is to provide an overview of the numerical solution of large- scale algebraic eigenvalue problems. The focus will be on a class of methods called Krylov subspace projection methods. The well-known Lanczos method is the premier member of this class. The Arnoldi method generalizes the Lanczos method to the nonsymmetric case. -
Krylov Subspaces
Lab 1 Krylov Subspaces Lab Objective: Discuss simple Krylov Subspace Methods for finding eigenvalues and show some interesting applications. One of the biggest difficulties in computational linear algebra is the amount of memory needed to store a large matrix and the amount of time needed to read its entries. Methods using Krylov subspaces avoid this difficulty by studying how a matrix acts on vectors, making it unnecessary in many cases to create the matrix itself. More specifically, we can construct a Krylov subspace just by knowing how a linear transformation acts on vectors, and with these subspaces we can closely approximate eigenvalues of the transformation and solutions to associated linear systems. The Arnoldi iteration is an algorithm for finding an orthonormal basis of a Krylov subspace. Its outputs can also be used to approximate the eigenvalues of the original matrix. The Arnoldi Iteration The order-N Krylov subspace of A generated by x is 2 n−1 Kn(A; x) = spanfx;Ax;A x;:::;A xg: If the vectors fx;Ax;A2x;:::;An−1xg are linearly independent, then they form a basis for Kn(A; x). However, this basis is usually far from orthogonal, and hence computations using this basis will likely be ill-conditioned. One way to find an orthonormal basis for Kn(A; x) would be to use the modi- fied Gram-Schmidt algorithm from Lab TODO on the set fx;Ax;A2x;:::;An−1xg. More efficiently, the Arnold iteration integrates the creation of fx;Ax;A2x;:::;An−1xg with the modified Gram-Schmidt algorithm, returning an orthonormal basis for Kn(A; x). -
Accelerating the LOBPCG Method on Gpus Using a Blocked Sparse Matrix Vector Product
Accelerating the LOBPCG method on GPUs using a blocked Sparse Matrix Vector Product Hartwig Anzt and Stanimire Tomov and Jack Dongarra Innovative Computing Lab University of Tennessee Knoxville, USA Email: [email protected], [email protected], [email protected] Abstract— the computing power of today’s supercomputers, often accel- erated by coprocessors like graphics processing units (GPUs), This paper presents a heterogeneous CPU-GPU algorithm design and optimized implementation for an entire sparse iter- becomes challenging. ative eigensolver – the Locally Optimal Block Preconditioned Conjugate Gradient (LOBPCG) – starting from low-level GPU While there exist numerous efforts to adapt iterative lin- data structures and kernels to the higher-level algorithmic choices ear solvers like Krylov subspace methods to coprocessor and overall heterogeneous design. Most notably, the eigensolver technology, sparse eigensolvers have so far remained out- leverages the high-performance of a new GPU kernel developed side the main focus. A possible explanation is that many for the simultaneous multiplication of a sparse matrix and a of those combine sparse and dense linear algebra routines, set of vectors (SpMM). This is a building block that serves which makes porting them to accelerators more difficult. Aside as a backbone for not only block-Krylov, but also for other from the power method, algorithms based on the Krylov methods relying on blocking for acceleration in general. The subspace idea are among the most commonly used general heterogeneous LOBPCG developed here reveals the potential of eigensolvers [1]. When targeting symmetric positive definite this type of eigensolver by highly optimizing all of its components, eigenvalue problems, the recently developed Locally Optimal and can be viewed as a benchmark for other SpMM-dependent applications. -
Iterative Methods for Linear System
Iterative methods for Linear System JASS 2009 Student: Rishi Patil Advisor: Prof. Thomas Huckle Outline ●Basics: Matrices and their properties Eigenvalues, Condition Number ●Iterative Methods Direct and Indirect Methods ●Krylov Subspace Methods Ritz Galerkin: CG Minimum Residual Approach : GMRES/MINRES Petrov-Gaelerkin Method: BiCG, QMR, CGS 1st April JASS 2009 2 Basics ●Linear system of equations Ax = b ●A Hermitian matrix (or self-adjoint matrix ) is a square matrix with complex entries which is equal to its own conjugate transpose, 3 2 + i that is, the element in the ith row and jth column is equal to the A = complex conjugate of the element in the jth row and ith column, for 2 − i 1 all indices i and j • Symmetric if a ij = a ji • Positive definite if, for every nonzero vector x XTAx > 0 • Quadratic form: 1 f( x) === xTAx −−− bTx +++ c 2 ∂ f( x) • Gradient of Quadratic form: ∂x 1 1 1 f' (x) = ⋮ = ATx + Ax − b ∂ 2 2 f( x) ∂xn 1st April JASS 2009 3 Various quadratic forms Positive-definite Negative-definite matrix matrix Singular Indefinite positive-indefinite matrix matrix 1st April JASS 2009 4 Various quadratic forms 1st April JASS 2009 5 Eigenvalues and Eigenvectors For any n×n matrix A, a scalar λ and a nonzero vector v that satisfy the equation Av =λv are said to be the eigenvalue and the eigenvector of A. ●If the matrix is symmetric , then the following properties hold: (a) the eigenvalues of A are real (b) eigenvectors associated with distinct eigenvalues are orthogonal ●The matrix A is positive definite (or positive semidefinite) if and only if all eigenvalues of A are positive (or nonnegative). -
Microbenchmarks in Big Data
M Microbenchmark Overview Microbenchmarks constitute the first line of per- Nicolas Poggi formance testing. Through them, we can ensure Databricks Inc., Amsterdam, NL, BarcelonaTech the proper and timely functioning of the different (UPC), Barcelona, Spain individual components that make up our system. The term micro, of course, depends on the prob- lem size. In BigData we broaden the concept Synonyms to cover the testing of large-scale distributed systems and computing frameworks. This chap- Component benchmark; Functional benchmark; ter presents the historical background, evolution, Test central ideas, and current key applications of the field concerning BigData. Definition Historical Background A microbenchmark is either a program or routine to measure and test the performance of a single Origins and CPU-Oriented Benchmarks component or task. Microbenchmarks are used to Microbenchmarks are closer to both hardware measure simple and well-defined quantities such and software testing than to competitive bench- as elapsed time, rate of operations, bandwidth, marking, opposed to application-level – macro or latency. Typically, microbenchmarks were as- – benchmarking. For this reason, we can trace sociated with the testing of individual software microbenchmarking influence to the hardware subroutines or lower-level hardware components testing discipline as can be found in Sumne such as the CPU and for a short period of time. (1974). Furthermore, we can also find influence However, in the BigData scope, the term mi- in the origins of software testing methodology crobenchmarking is broadened to include the during the 1970s, including works such cluster – group of networked computers – acting as Chow (1978). One of the first examples of as a single system, as well as the testing of a microbenchmark clearly distinguishable from frameworks, algorithms, logical and distributed software testing is the Whetstone benchmark components, for a longer period and larger data developed during the late 1960s and published sizes. -
Overview of the SPEC Benchmarks
9 Overview of the SPEC Benchmarks Kaivalya M. Dixit IBM Corporation “The reputation of current benchmarketing claims regarding system performance is on par with the promises made by politicians during elections.” Standard Performance Evaluation Corporation (SPEC) was founded in October, 1988, by Apollo, Hewlett-Packard,MIPS Computer Systems and SUN Microsystems in cooperation with E. E. Times. SPEC is a nonprofit consortium of 22 major computer vendors whose common goals are “to provide the industry with a realistic yardstick to measure the performance of advanced computer systems” and to educate consumers about the performance of vendors’ products. SPEC creates, maintains, distributes, and endorses a standardized set of application-oriented programs to be used as benchmarks. 489 490 CHAPTER 9 Overview of the SPEC Benchmarks 9.1 Historical Perspective Traditional benchmarks have failed to characterize the system performance of modern computer systems. Some of those benchmarks measure component-level performance, and some of the measurements are routinely published as system performance. Historically, vendors have characterized the performances of their systems in a variety of confusing metrics. In part, the confusion is due to a lack of credible performance information, agreement, and leadership among competing vendors. Many vendors characterize system performance in millions of instructions per second (MIPS) and millions of floating-point operations per second (MFLOPS). All instructions, however, are not equal. Since CISC machine instructions usually accomplish a lot more than those of RISC machines, comparing the instructions of a CISC machine and a RISC machine is similar to comparing Latin and Greek. 9.1.1 Simple CPU Benchmarks Truth in benchmarking is an oxymoron because vendors use benchmarks for marketing purposes. -
Hypervisors Vs. Lightweight Virtualization: a Performance Comparison
2015 IEEE International Conference on Cloud Engineering Hypervisors vs. Lightweight Virtualization: a Performance Comparison Roberto Morabito, Jimmy Kjällman, and Miika Komu Ericsson Research, NomadicLab Jorvas, Finland [email protected], [email protected], [email protected] Abstract — Virtualization of operating systems provides a container and alternative solutions. The idea is to quantify the common way to run different services in the cloud. Recently, the level of overhead introduced by these platforms and the lightweight virtualization technologies claim to offer superior existing gap compared to a non-virtualized environment. performance. In this paper, we present a detailed performance The remainder of this paper is structured as follows: in comparison of traditional hypervisor based virtualization and Section II, literature review and a brief description of all the new lightweight solutions. In our measurements, we use several technologies and platforms evaluated is provided. The benchmarks tools in order to understand the strengths, methodology used to realize our performance comparison is weaknesses, and anomalies introduced by these different platforms in terms of processing, storage, memory and network. introduced in Section III. The benchmark results are presented Our results show that containers achieve generally better in Section IV. Finally, some concluding remarks and future performance when compared with traditional virtual machines work are provided in Section V. and other recent solutions. Albeit containers offer clearly more dense deployment of virtual machines, the performance II. BACKGROUND AND RELATED WORK difference with other technologies is in many cases relatively small. In this section, we provide an overview of the different technologies included in the performance comparison. -
Power Measurement Tutorial for the Green500 List
Power Measurement Tutorial for the Green500 List R. Ge, X. Feng, H. Pyla, K. Cameron, W. Feng June 27, 2007 Contents 1 The Metric for Energy-Efficiency Evaluation 1 2 How to Obtain P¯(Rmax)? 2 2.1 The Definition of P¯(Rmax)...................................... 2 2.2 Deriving P¯(Rmax) from Unit Power . 2 2.3 Measuring Unit Power . 3 3 The Measurement Procedure 3 3.1 Equipment Check List . 4 3.2 Software Installation . 4 3.3 Hardware Connection . 4 3.4 Power Measurement Procedure . 5 4 Appendix 6 4.1 Frequently Asked Questions . 6 4.2 Resources . 6 1 The Metric for Energy-Efficiency Evaluation This tutorial serves as a practical guide for measuring the computer system power that is required as part of a Green500 submission. It describes the basic procedures to be followed in order to measure the power consumption of a supercomputer. A supercomputer that appears on The TOP500 List can easily consume megawatts of electric power. This power consumption may lead to operating costs that exceed acquisition costs as well as intolerable system failure rates. In recent years, we have witnessed an increasingly stronger movement towards energy-efficient computing systems in academia, government, and industry. Thus, the purpose of the Green500 List is to provide a ranking of the most energy-efficient supercomputers in the world and serve as a complementary view to the TOP500 List. However, as pointed out in [1, 2], identifying a single objective metric for energy efficiency in supercom- puters is a difficult task. Based on [1, 2] and given the already existing use of the “performance per watt” metric, the Green500 List uses “performance per watt” (PPW) as its metric to rank the energy efficiency of supercomputers. -
Implicitly Restarted Arnoldi/Lanczos Methods for Large Scale Eigenvalue Calculations
https://ntrs.nasa.gov/search.jsp?R=19960048075 2020-06-16T03:31:45+00:00Z NASA Contractor Report 198342 /" ICASE Report No. 96-40 J ICA IMPLICITLY RESTARTED ARNOLDI/LANCZOS METHODS FOR LARGE SCALE EIGENVALUE CALCULATIONS Danny C. Sorensen NASA Contract No. NASI-19480 May 1996 Institute for Computer Applications in Science and Engineering NASA Langley Research Center Hampton, VA 23681-0001 Operated by Universities Space Research Association National Aeronautics and Space Administration Langley Research Center Hampton, Virginia 23681-0001 IMPLICITLY RESTARTED ARNOLDI/LANCZOS METHODS FOR LARGE SCALE EIGENVALUE CALCULATIONS Danny C. Sorensen 1 Department of Computational and Applied Mathematics Rice University Houston, TX 77251 sorensen@rice, edu ABSTRACT Eigenvalues and eigenfunctions of linear operators are important to many areas of ap- plied mathematics. The ability to approximate these quantities numerically is becoming increasingly important in a wide variety of applications. This increasing demand has fu- eled interest in the development of new methods and software for the numerical solution of large-scale algebraic eigenvalue problems. In turn, the existence of these new methods and software, along with the dramatically increased computational capabilities now avail- able, has enabled the solution of problems that would not even have been posed five or ten years ago. Until very recently, software for large-scale nonsymmetric problems was virtually non-existent. Fortunately, the situation is improving rapidly. The purpose of this article is to provide an overview of the numerical solution of large- scale algebraic eigenvalue problems. The focus will be on a class of methods called Krylov subspace projection methods. The well-known Lanczos method is the premier member of this class. -
Limited Memory Block Krylov Subspace Optimization for Computing Dominant Singular Value Decompositions
Limited Memory Block Krylov Subspace Optimization for Computing Dominant Singular Value Decompositions Xin Liu∗ Zaiwen Weny Yin Zhangz March 22, 2012 Abstract In many data-intensive applications, the use of principal component analysis (PCA) and other related techniques is ubiquitous for dimension reduction, data mining or other transformational purposes. Such transformations often require efficiently, reliably and accurately computing dominant singular value de- compositions (SVDs) of large unstructured matrices. In this paper, we propose and study a subspace optimization technique to significantly accelerate the classic simultaneous iteration method. We analyze the convergence of the proposed algorithm, and numerically compare it with several state-of-the-art SVD solvers under the MATLAB environment. Extensive computational results show that on a wide range of large unstructured matrices, the proposed algorithm can often provide improved efficiency or robustness over existing algorithms. Keywords. subspace optimization, dominant singular value decomposition, Krylov subspace, eigen- value decomposition 1 Introduction Singular value decomposition (SVD) is a fundamental and enormously useful tool in matrix computations, such as determining the pseudo-inverse, the range or null space, or the rank of a matrix, solving regular or total least squares data fitting problems, or computing low-rank approximations to a matrix, just to mention a few. The need for computing SVDs also frequently arises from diverse fields in statistics, signal processing, data mining or compression, and from various dimension-reduction models of large-scale dynamic systems. Usually, instead of acquiring all the singular values and vectors of a matrix, it suffices to compute a set of dominant (i.e., the largest) singular values and their corresponding singular vectors in order to obtain the most valuable and relevant information about the underlying dataset or system. -
The High Performance Linpack (HPL) Benchmark Evaluation on UTP High Performance Computing Cluster by Wong Chun Shiang 16138 Diss
The High Performance Linpack (HPL) Benchmark Evaluation on UTP High Performance Computing Cluster By Wong Chun Shiang 16138 Dissertation submitted in partial fulfilment of the requirements for the Bachelor of Technology (Hons) (Information and Communications Technology) MAY 2015 Universiti Teknologi PETRONAS Bandar Seri Iskandar 31750 Tronoh Perak Darul Ridzuan CERTIFICATION OF APPROVAL The High Performance Linpack (HPL) Benchmark Evaluation on UTP High Performance Computing Cluster by Wong Chun Shiang 16138 A project dissertation submitted to the Information & Communication Technology Programme Universiti Teknologi PETRONAS In partial fulfillment of the requirement for the BACHELOR OF TECHNOLOGY (Hons) (INFORMATION & COMMUNICATION TECHNOLOGY) Approved by, ____________________________ (DR. IZZATDIN ABDUL AZIZ) UNIVERSITI TEKNOLOGI PETRONAS TRONOH, PERAK MAY 2015 ii CERTIFICATION OF ORIGINALITY This is to certify that I am responsible for the work submitted in this project, that the original work is my own except as specified in the references and acknowledgements, and that the original work contained herein have not been undertaken or done by unspecified sources or persons. ________________ WONG CHUN SHIANG iii ABSTRACT UTP High Performance Computing Cluster (HPCC) is a collection of computing nodes using commercially available hardware interconnected within a network to communicate among the nodes. This campus wide cluster is used by researchers from internal UTP and external parties to compute intensive applications. However, the HPCC has never been benchmarked before. It is imperative to carry out a performance study to measure the true computing ability of this cluster. This project aims to test the performance of a campus wide computing cluster using a selected benchmarking tool, the High Performance Linkpack (HPL).