Boost.SIMD: Generic Programming for Portable Simdization
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(LINUX) Computer in Three Parts
Science on a (LINUX) computer in three parts Introductory short couse, Part II Thorsten Becker University of Southern California, Los Angeles September 2007 The first part dealt with ● UNIX: what and why ● File system, Window managers ● Shell environment ● Editing files ● Command line tools ● Scripts and GUIs ● Virtualization Contents part II ● Typesetting ● Programming – common languages – philosophy – compiling, debugging, make, version control – C and F77 interfacing – libraries and packages ● Number crunching ● Visualization tools Programming: Traditional languages in the natural sciences ● Fortran: higher level, good for math – F77: legacy, don't use (but know how to read) – F90/F95: nice vector features, finally implements C capabilities (structures, memory allocation) ● C: low level (e.g. pointers), better structured – very close to UNIX philosophy – structures offer nice way of modular programming, see Wikipedia on C ● I recommend F95, and use C happily myself Programming: Some Languages that haven't completely made it to scientific computing ● C++: object oriented programming model – reusable objects with methods and such – can be partly realized by modular programming in C ● Java: what's good for commercial projects (or smart, or elegant) doesn't have to be good for scientific computing ● Concern about portability as well as general access Programming: Compromises ● Python – Object oriented – Interpreted – Interfaces easily with F90/C – Numerous scientific packages Programming: Other interpreted, high- abstraction languages -
Threads Chapter 4
Threads Chapter 4 Reading: 4.1,4.4, 4.5 1 Process Characteristics ● Unit of resource ownership - process is allocated: ■ a virtual address space to hold the process image ■ control of some resources (files, I/O devices...) ● Unit of dispatching - process is an execution path through one or more programs ■ execution may be interleaved with other process ■ the process has an execution state and a dispatching priority 2 Process Characteristics ● These two characteristics are treated independently by some recent OS ● The unit of dispatching is usually referred to a thread or a lightweight process ● The unit of resource ownership is usually referred to as a process or task 3 Multithreading vs. Single threading ● Multithreading: when the OS supports multiple threads of execution within a single process ● Single threading: when the OS does not recognize the concept of thread ● MS-DOS support a single user process and a single thread ● UNIX supports multiple user processes but only supports one thread per process ● Solaris /NT supports multiple threads 4 Threads and Processes 5 Processes Vs Threads ● Have a virtual address space which holds the process image ■ Process: an address space, an execution context ■ Protected access to processors, other processes, files, and I/O Class threadex{ resources Public static void main(String arg[]){ ■ Context switch between Int x=0; processes expensive My_thread t1= new my_thread(x); t1.start(); ● Threads of a process execute in Thr_wait(); a single address space System.out.println(x) ■ Global variables are -
Some Notes on BLAS, SIMD, MIC and GPGPU (For Octave and Matlab)
Some Notes on BLAS, SIMD, MIC and GPGPU (for Octave and Matlab) Christian Himpe ([email protected]) WWU Münster Institute for Computational and Applied Mathematics Software-Tools für die Numerische Mathematik 15.10.2014 About1 BLAS & LAPACK Affinity SIMD Automatic Offloading 1 Get your Buzzword-Bingo ready! BLAS & LAPACK BLAS (Basic Linear Algebra System) Level 1: vector-vector operations (dot-product, vector norms, generalized vector addition) Level 2: matrix-vector operations (generalized matrix-vector multiplication) Level 3: matrix-matrix operations (generalized matrix-matrix multiplication) LAPACK (Linear Algebra Package) Matrix Factorizations: LU, QR, Cholesky, Schur Least-Squares: LLS, LSE, GLM Eigenproblems: SEP, NEP, SVD Default (un-optimized) netlib reference implementation. Used by Octave, Matlab, SciPy/NumPy (Python), Julia, R. MKL Intel’s implementation of BLAS and LAPACK. MKL (Math Kernel Library) can offload computations to XeonPhi can use OpenMP provides additionally FFT, libm and 1D-interpolation Current Version: 11.0.5 (automatic offloading to Phis) Costs (we have it, and Matlab ships with it, too) Go to: https://software.intel.com/en-us/intel-mkl ACML AMD doesn’t want to be left out. ACML (AMD Core Math Libraries) Can use OpenCL for automatic offloading to GPUs Special version to exploit FMA(4) instructions Choice of compiled binaries (GFortran, Intel Fortran, Open64, PGI) Current Version: 6 (automatic offloading to GPUs) Free (but not open source) Go to: http://developer.amd.com/tools-and-sdks/ cpu-development/amd-core-math-library-acml OpenBLAS Open Source, the third kind. OpenBLAS Fork of GotoBLAS Good performance for dense operations (close to the MKL) Can use OpenMP and is compiled for specific architecture Current Version: 0.2.11 Open source (!) Go to: http://github.com/xianyi/OpenBLAS FlexiBLAS So many BLAS implementations, so little time.. -
Lecture 10: Introduction to Openmp (Part 2)
Lecture 10: Introduction to OpenMP (Part 2) 1 Performance Issues I • C/C++ stores matrices in row-major fashion. • Loop interchanges may increase cache locality { … #pragma omp parallel for for(i=0;i< N; i++) { for(j=0;j< M; j++) { A[i][j] =B[i][j] + C[i][j]; } } } • Parallelize outer-most loop 2 Performance Issues II • Move synchronization points outwards. The inner loop is parallelized. • In each iteration step of the outer loop, a parallel region is created. This causes parallelization overhead. { … for(i=0;i< N; i++) { #pragma omp parallel for for(j=0;j< M; j++) { A[i][j] =B[i][j] + C[i][j]; } } } 3 Performance Issues III • Avoid parallel overhead at low iteration counts { … #pragma omp parallel for if(M > 800) for(j=0;j< M; j++) { aa[j] =alpha*bb[j] + cc[j]; } } 4 C++: Random Access Iterators Loops • Parallelization of random access iterator loops is supported void iterator_example(){ std::vector vec(23); std::vector::iterator it; #pragma omp parallel for default(none) shared(vec) for(it=vec.begin(); it< vec.end(); it++) { // do work with it // } } 5 Conditional Compilation • Keep sequential and parallel programs as a single source code #if def _OPENMP #include “omp.h” #endif Main() { #ifdef _OPENMP omp_set_num_threads(3); #endif for(i=0;i< N; i++) { #pragma omp parallel for for(j=0;j< M; j++) { A[i][j] =B[i][j] + C[i][j]; } } } 6 Be Careful with Data Dependences • Whenever a statement in a program reads or writes a memory location and another statement reads or writes the same memory location, and at least one of the two statements writes the location, then there is a data dependence on that memory location between the two statements. -
The Problem with Threads
The Problem with Threads Edward A. Lee Electrical Engineering and Computer Sciences University of California at Berkeley Technical Report No. UCB/EECS-2006-1 http://www.eecs.berkeley.edu/Pubs/TechRpts/2006/EECS-2006-1.html January 10, 2006 Copyright © 2006, by the author(s). All rights reserved. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission. Acknowledgement This work was supported in part by the Center for Hybrid and Embedded Software Systems (CHESS) at UC Berkeley, which receives support from the National Science Foundation (NSF award No. CCR-0225610), the State of California Micro Program, and the following companies: Agilent, DGIST, General Motors, Hewlett Packard, Infineon, Microsoft, and Toyota. The Problem with Threads Edward A. Lee Professor, Chair of EE, Associate Chair of EECS EECS Department University of California at Berkeley Berkeley, CA 94720, U.S.A. [email protected] January 10, 2006 Abstract Threads are a seemingly straightforward adaptation of the dominant sequential model of computation to concurrent systems. Languages require little or no syntactic changes to sup- port threads, and operating systems and architectures have evolved to efficiently support them. Many technologists are pushing for increased use of multithreading in software in order to take advantage of the predicted increases in parallelism in computer architectures. -
Parallel Programming Models for Dense Linear Algebra on Heterogeneous Systems
DOI: 10.14529/jsfi150405 Parallel Programming Models for Dense Linear Algebra on Heterogeneous Systems M. Abalenkovs1, A. Abdelfattah2, J. Dongarra 1,2,3, M. Gates2, A. Haidar2, J. Kurzak2, P. Luszczek2, S. Tomov2, I. Yamazaki2, A. YarKhan2 c The Authors 2015. This paper is published with open access at SuperFri.org We present a review of the current best practices in parallel programming models for dense linear algebra (DLA) on heterogeneous architectures. We consider multicore CPUs, stand alone manycore coprocessors, GPUs, and combinations of these. Of interest is the evolution of the programming models for DLA libraries – in particular, the evolution from the popular LAPACK and ScaLAPACK libraries to their modernized counterparts PLASMA (for multicore CPUs) and MAGMA (for heterogeneous architectures), as well as other programming models and libraries. Besides providing insights into the programming techniques of the libraries considered, we outline our view of the current strengths and weaknesses of their programming models – especially in regards to hardware trends and ease of programming high-performance numerical software that current applications need – in order to motivate work and future directions for the next generation of parallel programming models for high-performance linear algebra libraries on heterogeneous systems. Keywords: Programming models, runtime, HPC, GPU, multicore, dense linear algebra. Introduction Parallelism in today’s computer architectures is pervasive – not only in systems from large supercomputers to laptops, but also in small portable devices like smart phones and watches. Along with parallelism, the level of heterogeneity in modern computing systems is also gradually increasing. Multicore CPUs are often combined with discrete high-performance accelerators like graphics processing units (GPUs) and coprocessors like Intel’s Xeon Phi, but are also included as integrated parts with system-on-chip (SoC) platforms, as in the AMD Fusion family of ap- plication processing units (APUs) or the NVIDIA Tegra mobile family of devices. -
Modifiable Array Data Structures for Mesh Topology
Modifiable Array Data Structures for Mesh Topology Dan Ibanez Mark S Shephard February 27, 2016 Abstract Topological data structures are useful in many areas, including the various mesh data structures used in finite element applications. Based on the graph-theoretic foundation for these data structures, we begin with a generic modifiable graph data structure and apply successive optimiza- tions leading to a family of mesh data structures. The results are compact array-based mesh structures that can be modified in constant time. Spe- cific implementations for finite elements and graphics are studied in detail and compared to the current state of the art. 1 Introduction An unstructured mesh simulation code relies heavily on multiple core capabili- ties to deal with the mesh itself, and the range of features available at this level constrain the capabilities of the simulation as a whole. As such, the long-term goal towards which this paper contributes is the development of a mesh data structure with the following capabilities: 1. The flexibility to deal with evolving meshes 2. A highly scalable implementation for distributed memory computers 3. The ability to represent any of the conforming meshes typically used by Finite Element (FE) and Finite Volume (FV) methods 4. Minimize memory use 5. Maximize locality of storage 6. The ability to parallelize work inside supercomputer nodes with hybrid architecture such as accelerators This paper focuses on the first five goals; the sixth will be the subject of a future publication. In particular, we present a derivation for a family of structures with these properties: 1 1. -
AMD Core Math Library (ACML)
AMD Core Math Library (ACML) Version 4.2.0 Copyright c 2003-2008 Advanced Micro Devices, Inc., Numerical Algorithms Group Ltd. AMD, the AMD Arrow logo, AMD Opteron, AMD Athlon and combinations thereof are trademarks of Advanced Micro Devices, Inc. i Short Contents 1 Introduction................................... 1 2 General Information ............................. 2 3 BLAS: Basic Linear Algebra Subprograms ............. 19 4 LAPACK: Package of Linear Algebra Subroutines ........ 20 5 Fast Fourier Transforms (FFTs) .................... 24 6 Random Number Generators....................... 75 7 ACML MV: Fast Math and Fast Vector Math Library .... 163 8 References .................................. 229 Subject Index ................................... 230 Routine Index ................................... 233 ii Table of Contents 1 Introduction ............................... 1 2 General Information ....................... 2 2.1 Determining the best ACML version for your system ........... 2 2.2 Accessing the Library (Linux) ................................ 4 2.2.1 Accessing the Library under Linux using GNU gfortran/gcc ......................................................... 4 2.2.2 Accessing the Library under Linux using PGI compilers pgf77/pgf90/pgcc ......................................... 5 2.2.3 Accessing the Library under Linux using PathScale compilers pathf90/pathcc ........................................... 6 2.2.4 Accessing the Library under Linux using the NAGWare f95 compiler................................................. -
CUDA Binary Utilities
CUDA Binary Utilities Application Note DA-06762-001_v11.4 | September 2021 Table of Contents Chapter 1. Overview..............................................................................................................1 1.1. What is a CUDA Binary?...........................................................................................................1 1.2. Differences between cuobjdump and nvdisasm......................................................................1 Chapter 2. cuobjdump.......................................................................................................... 3 2.1. Usage......................................................................................................................................... 3 2.2. Command-line Options.............................................................................................................5 Chapter 3. nvdisasm.............................................................................................................8 3.1. Usage......................................................................................................................................... 8 3.2. Command-line Options...........................................................................................................14 Chapter 4. Instruction Set Reference................................................................................ 17 4.1. Kepler Instruction Set.............................................................................................................17 -
Lithe: Enabling Efficient Composition of Parallel Libraries
BERKELEY PAR LAB Lithe: Enabling Efficient Composition of Parallel Libraries Heidi Pan, Benjamin Hindman, Krste Asanović [email protected] {benh, krste}@eecs.berkeley.edu Massachusetts Institute of Technology UC Berkeley HotPar Berkeley, CA March 31, 2009 1 How to Build Parallel Apps? BERKELEY PAR LAB Functionality: or or or App Resource Management: OS Hardware Core 0 Core 1 Core 2 Core 3 Core 4 Core 5 Core 6 Core 7 Need both programmer productivity and performance! 2 Composability is Key to Productivity BERKELEY PAR LAB App 1 App 2 App sort sort bubble quick sort sort code reuse modularity same library implementation, different apps same app, different library implementations Functional Composability 3 Composability is Key to Productivity BERKELEY PAR LAB fast + fast fast fast + faster fast(er) Performance Composability 4 Talk Roadmap BERKELEY PAR LAB Problem: Efficient parallel composability is hard! Solution: . Harts . Lithe Evaluation 5 Motivational Example BERKELEY PAR LAB Sparse QR Factorization (Tim Davis, Univ of Florida) Column Elimination SPQR Tree Frontal Matrix Factorization MKL TBB OpenMP OS Hardware System Stack Software Architecture 6 Out-of-the-Box Performance BERKELEY PAR LAB Performance of SPQR on 16-core Machine Out-of-the-Box sequential Time (sec) Time Input Matrix 7 Out-of-the-Box Libraries Oversubscribe the Resources BERKELEY PAR LAB TX TYTX TYTX TYTX A[0] TYTX A[0] TYTX A[0] TYTX A[0] TYTX TYA[0] A[0] A[0]A[0] +Z +Z +Z +Z +Z +Z +Z +ZA[1] A[1] A[1] A[1] A[1] A[1] A[1]A[1] A[2] A[2] A[2] A[2] A[2] A[2] A[2]A[2] -
Thread Scheduling in Multi-Core Operating Systems Redha Gouicem
Thread Scheduling in Multi-core Operating Systems Redha Gouicem To cite this version: Redha Gouicem. Thread Scheduling in Multi-core Operating Systems. Computer Science [cs]. Sor- bonne Université, 2020. English. tel-02977242 HAL Id: tel-02977242 https://hal.archives-ouvertes.fr/tel-02977242 Submitted on 24 Oct 2020 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. Ph.D thesis in Computer Science Thread Scheduling in Multi-core Operating Systems How to Understand, Improve and Fix your Scheduler Redha GOUICEM Sorbonne Université Laboratoire d’Informatique de Paris 6 Inria Whisper Team PH.D.DEFENSE: 23 October 2020, Paris, France JURYMEMBERS: Mr. Pascal Felber, Full Professor, Université de Neuchâtel Reviewer Mr. Vivien Quéma, Full Professor, Grenoble INP (ENSIMAG) Reviewer Mr. Rachid Guerraoui, Full Professor, École Polytechnique Fédérale de Lausanne Examiner Ms. Karine Heydemann, Associate Professor, Sorbonne Université Examiner Mr. Etienne Rivière, Full Professor, University of Louvain Examiner Mr. Gilles Muller, Senior Research Scientist, Inria Advisor Mr. Julien Sopena, Associate Professor, Sorbonne Université Advisor ABSTRACT In this thesis, we address the problem of schedulers for multi-core architectures from several perspectives: design (simplicity and correct- ness), performance improvement and the development of application- specific schedulers. -
35.232-2016.43 Lamees Elhiny.Pdf
LOAD PARTITIONING FOR MATRIX-MATRIX MULTIPLICATION ON A CLUSTER OF CPU-GPU NODES USING THE DIVISIBLE LOAD PARADIGM by Lamees Elhiny A Thesis Presented to the Faculty of the American University of Sharjah College of Engineering in Partial Fulfillment of the Requirements for the Degree of Master of Science in Computer Engineering Sharjah, United Arab Emirates November 2016 c 2016. Lamees Elhiny. All rights reserved. Approval Signatures We, the undersigned, approve the Master’s Thesis of Lamees Elhiny Thesis Title: Load Partitioning for Matrix-Matrix Multiplication on a Cluster of CPU- GPU Nodes Using the Divisible Load Paradigm Signature Date of Signature (dd/mm/yyyy) ___________________________ _______________ Dr. Gerassimos Barlas Professor, Department of Computer Science and Engineering Thesis Advisor ___________________________ _______________ Dr. Khaled El-Fakih Associate Professor, Department of Computer Science and Engineering Thesis Committee Member ___________________________ _______________ Dr. Naoufel Werghi Associate Professor, Electrical and Computer Engineering Department Khalifa University of Science, Technology & Research (KUSTAR) Thesis Committee Member ___________________________ _______________ Dr. Fadi Aloul Head, Department of Computer Science and Engineering ___________________________ _______________ Dr. Mohamed El-Tarhuni Associate Dean, College of Engineering ___________________________ _______________ Dr. Richard Schoephoerster Dean, College of Engineering ___________________________ _______________ Dr. Khaled Assaleh Interim Vice Provost for Research and Graduate Studies Acknowledgements I would like to express my sincere gratitude to my thesis advisor, Dr. Gerassi- mos Barlas, for his guidance at every step throughout the thesis. I am thankful to Dr. Assim Sagahyroon, and to the Department of Computer Science & Engineering as well as the American University of Sharjah for offering me the Graduate Teaching Assistantship, which allowed me to pursue my graduate studies.