Tangent: Automatic Differentiation Using Source-Code Transformation for Dynamically Typed Array Programming
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Python on Gpus (Work in Progress!)
Python on GPUs (work in progress!) Laurie Stephey GPUs for Science Day, July 3, 2019 Rollin Thomas, NERSC Lawrence Berkeley National Laboratory Python is friendly and popular Screenshots from: https://www.tiobe.com/tiobe-index/ So you want to run Python on a GPU? You have some Python code you like. Can you just run it on a GPU? import numpy as np from scipy import special import gpu ? Unfortunately no. What are your options? Right now, there is no “right” answer ● CuPy ● Numba ● pyCUDA (https://mathema.tician.de/software/pycuda/) ● pyOpenCL (https://mathema.tician.de/software/pyopencl/) ● Rewrite kernels in C, Fortran, CUDA... DESI: Our case study Now Perlmutter 2020 Goal: High quality output spectra Spectral Extraction CuPy (https://cupy.chainer.org/) ● Developed by Chainer, supported in RAPIDS ● Meant to be a drop-in replacement for NumPy ● Some, but not all, NumPy coverage import numpy as np import cupy as cp cpu_ans = np.abs(data) #same thing on gpu gpu_data = cp.asarray(data) gpu_temp = cp.abs(gpu_data) gpu_ans = cp.asnumpy(gpu_temp) Screenshot from: https://docs-cupy.chainer.org/en/stable/reference/comparison.html eigh in CuPy ● Important function for DESI ● Compared CuPy eigh on Cori Volta GPU to Cori Haswell and Cori KNL ● Tried “divide-and-conquer” approach on both CPU and GPU (1, 2, 5, 10 divisions) ● Volta wins only at very large matrix sizes ● Major pro: eigh really easy to use in CuPy! legval in CuPy ● Easy to convert from NumPy arrays to CuPy arrays ● This function is ~150x slower than the cpu version! ● This implies there -
Introduction Shrinkage Factor Reference
Comparison study for implementation efficiency of CUDA GPU parallel computation with the fast iterative shrinkage-thresholding algorithm Younsang Cho, Donghyeon Yu Department of Statistics, Inha university 4. TensorFlow functions in Python (TF-F) Introduction There are some functions executed on GPU in TensorFlow. So, we implemented our algorithm • Parallel computation using graphics processing units (GPUs) gets much attention and is just using that functions. efficient for single-instruction multiple-data (SIMD) processing. 5. Neural network with TensorFlow in Python (TF-NN) • Theoretical computation capacity of the GPU device has been growing fast and is much higher Neural network model is flexible, and the LASSO problem can be represented as a simple than that of the CPU nowadays (Figure 1). neural network with an ℓ1-regularized loss function • There are several platforms for conducting parallel computation on GPUs using compute 6. Using dynamic link library in Python (P-DLL) unified device architecture (CUDA) developed by NVIDIA. (Python, PyCUDA, Tensorflow, etc. ) As mentioned before, we can load DLL files, which are written in CUDA C, using "ctypes.CDLL" • However, it is unclear what platform is the most efficient for CUDA. that is a built-in function in Python. 7. Using dynamic link library in R (R-DLL) We can also load DLL files, which are written in CUDA C, using "dyn.load" in R. FISTA (Fast Iterative Shrinkage-Thresholding Algorithm) We consider FISTA (Beck and Teboulle, 2009) with backtracking as the following: " Step 0. Take �! > 0, some � > 1, and �! ∈ ℝ . Set �# = �!, �# = 1. %! Step k. � ≥ 1 Find the smallest nonnegative integers �$ such that with �g = � �$&# � �(' �$ ≤ �(' �(' �$ , �$ . -
R from a Programmer's Perspective Accompanying Manual for an R Course Held by M
DSMZ R programming course R from a programmer's perspective Accompanying manual for an R course held by M. Göker at the DSMZ, 11/05/2012 & 25/05/2012. Slightly improved version, 10/09/2012. This document is distributed under the CC BY 3.0 license. See http://creativecommons.org/licenses/by/3.0 for details. Introduction The purpose of this course is to cover aspects of R programming that are either unlikely to be covered elsewhere or likely to be surprising for programmers who have worked with other languages. The course thus tries not be comprehensive but sort of complementary to other sources of information. Also, the material needed to by compiled in short time and perhaps suffers from important omissions. For the same reason, potential participants should not expect a fully fleshed out presentation but a combination of a text-only document (this one) with example code comprising the solutions of the exercises. The topics covered include R's general features as a programming language, a recapitulation of R's type system, advanced coding of functions, error handling, the use of attributes in R, object-oriented programming in the S3 system, and constructing R packages (in this order). The expected audience comprises R users whose own code largely consists of self-written functions, as well as programmers who are fluent in other languages and have some experience with R. Interactive users of R without programming experience elsewhere are unlikely to benefit from this course because quite a few programming skills cannot be covered here but have to be presupposed. -
Parallel Functional Programming with APL
Parallel Functional Programming, APL Lecture 1 Parallel Functional Programming with APL Martin Elsman Department of Computer Science University of Copenhagen DIKU December 19, 2016 Martin Elsman (DIKU) Parallel Functional Programming, APL Lecture 1 December 19, 2016 1 / 18 Outline 1 Outline Course Outline 2 Introduction to APL What is APL APL Implementations and Material APL Scalar Operations APL (1-Dimensional) Vector Computations Declaring APL Functions (dfns) APL Multi-Dimensional Arrays Iterations Declaring APL Operators Function Trains Examples Reading Martin Elsman (DIKU) Parallel Functional Programming, APL Lecture 1 December 19, 2016 2 / 18 Outline Course Outline Teachers Martin Elsman (ME), Ken Friis Larsen (KFL), Andrzej Filinski (AF), and Troels Henriksen (TH) Location Lectures in Small Aud, Universitetsparken 1 (UP1); Labs in Old Library, UP1 Course Description See http://kurser.ku.dk/course/ndak14009u/2016-2017 Course Outline Week 47 48 49 50 51 1–3 Mon 13–15 Intro, Futhark Parallel SNESL APL (ME) Project Futhark (ME) Haskell (AF) (ME) (KFL) Mon 15–17 Lab Lab Lab Lab Project Wed 13–15 Futhark Parallel SNESL Invited APL Project (ME) Haskell (AF) Lecture (ME) / (KFL) (John Projects Reppy) Martin Elsman (DIKU) Parallel Functional Programming, APL Lecture 1 December 19, 2016 3 / 18 Introduction to APL What is APL APL—An Ancient Array Programming Language—But Still Used! Pioneered by Ken E. Iverson in the 1960’s. E. Dijkstra: “APL is a mistake, carried through to perfection.” There are quite a few APL programmers around (e.g., HIPERFIT partners). Very concise notation for expressing array operations. Has a large set of functional, essentially parallel, multi- dimensional, second-order array combinators. -
Prototyping and Developing GPU-Accelerated Solutions with Python and CUDA Luciano Martins and Robert Sohigian, 2018-11-22 Introduction to Python
Prototyping and Developing GPU-Accelerated Solutions with Python and CUDA Luciano Martins and Robert Sohigian, 2018-11-22 Introduction to Python GPU-Accelerated Computing NVIDIA® CUDA® technology Why Use Python with GPUs? Agenda Methods: PyCUDA, Numba, CuPy, and scikit-cuda Summary Q&A 2 Introduction to Python Released by Guido van Rossum in 1991 The Zen of Python: Beautiful is better than ugly. Explicit is better than implicit. Simple is better than complex. Complex is better than complicated. Flat is better than nested. Interpreted language (CPython, Jython, ...) Dynamically typed; based on objects 3 Introduction to Python Small core structure: ~30 keywords ~ 80 built-in functions Indentation is a pretty serious thing Dynamically typed; based on objects Binds to many different languages Supports GPU acceleration via modules 4 Introduction to Python 5 Introduction to Python 6 Introduction to Python 7 GPU-Accelerated Computing “[T]the use of a graphics processing unit (GPU) together with a CPU to accelerate deep learning, analytics, and engineering applications” (NVIDIA) Most common GPU-accelerated operations: Large vector/matrix operations (Basic Linear Algebra Subprograms - BLAS) Speech recognition Computer vision 8 GPU-Accelerated Computing Important concepts for GPU-accelerated computing: Host ― the machine running the workload (CPU) Device ― the GPUs inside of a host Kernel ― the code part that runs on the GPU SIMT ― Single Instruction Multiple Threads 9 GPU-Accelerated Computing 10 GPU-Accelerated Computing 11 CUDA Parallel computing -
Programming Language
Programming language A programming language is a formal language, which comprises a set of instructions that produce various kinds of output. Programming languages are used in computer programming to implement algorithms. Most programming languages consist of instructions for computers. There are programmable machines that use a set of specific instructions, rather than general programming languages. Early ones preceded the invention of the digital computer, the first probably being the automatic flute player described in the 9th century by the brothers Musa in Baghdad, during the Islamic Golden Age.[1] Since the early 1800s, programs have been used to direct the behavior of machines such as Jacquard looms, music boxes and player pianos.[2] The programs for these The source code for a simple computer program written in theC machines (such as a player piano's scrolls) did not programming language. When compiled and run, it will give the output "Hello, world!". produce different behavior in response to different inputs or conditions. Thousands of different programming languages have been created, and more are being created every year. Many programming languages are written in an imperative form (i.e., as a sequence of operations to perform) while other languages use the declarative form (i.e. the desired result is specified, not how to achieve it). The description of a programming language is usually split into the two components ofsyntax (form) and semantics (meaning). Some languages are defined by a specification document (for example, theC programming language is specified by an ISO Standard) while other languages (such as Perl) have a dominant implementation that is treated as a reference. -
RAL-TR-1998-060 Co-Array Fortran for Parallel Programming
RAL-TR-1998-060 Co-Array Fortran for parallel programming 1 by R. W. Numrich23 and J. K. Reid Abstract Co-Array Fortran, formerly known as F−− , is a small extension of Fortran 95 for parallel processing. A Co-Array Fortran program is interpreted as if it were replicated a number of times and all copies were executed asynchronously. Each copy has its own set of data objects and is termed an image. The array syntax of Fortran 95 is extended with additional trailing subscripts in square brackets to give a clear and straightforward representation of any access to data that is spread across images. References without square brackets are to local data, so code that can run independently is uncluttered. Only where there are square brackets, or where there is a procedure call and the procedure contains square brackets, is communication between images involved. There are intrinsic procedures to synchronize images, return the number of images, and return the index of the current image. We introduce the extension; give examples to illustrate how clear, powerful, and flexible it can be; and provide a technical definition. Categories and subject descriptors: D.3 [PROGRAMMING LANGUAGES]. General Terms: Parallel programming. Additional Key Words and Phrases: Fortran. Department for Computation and Information, Rutherford Appleton Laboratory, Oxon OX11 0QX, UK August 1998. 1 Available by anonymous ftp from matisa.cc.rl.ac.uk in directory pub/reports in the file nrRAL98060.ps.gz 2 Silicon Graphics, Inc., 655 Lone Oak Drive, Eagan, MN 55121, USA. Email: -
Programming the Capabilities of the PC Have Changed Greatly Since the Introduction of Electronic Computers
1 www.onlineeducation.bharatsevaksamaj.net www.bssskillmission.in INTRODUCTION TO PROGRAMMING LANGUAGE Topic Objective: At the end of this topic the student will be able to understand: History of Computer Programming C++ Definition/Overview: Overview: A personal computer (PC) is any general-purpose computer whose original sales price, size, and capabilities make it useful for individuals, and which is intended to be operated directly by an end user, with no intervening computer operator. Today a PC may be a desktop computer, a laptop computer or a tablet computer. The most common operating systems are Microsoft Windows, Mac OS X and Linux, while the most common microprocessors are x86-compatible CPUs, ARM architecture CPUs and PowerPC CPUs. Software applications for personal computers include word processing, spreadsheets, databases, games, and myriad of personal productivity and special-purpose software. Modern personal computers often have high-speed or dial-up connections to the Internet, allowing access to the World Wide Web and a wide range of other resources. Key Points: 1. History of ComputeWWW.BSSVE.INr Programming The capabilities of the PC have changed greatly since the introduction of electronic computers. By the early 1970s, people in academic or research institutions had the opportunity for single-person use of a computer system in interactive mode for extended durations, although these systems would still have been too expensive to be owned by a single person. The introduction of the microprocessor, a single chip with all the circuitry that formerly occupied large cabinets, led to the proliferation of personal computers after about 1975. Early personal computers - generally called microcomputers - were sold often in Electronic kit form and in limited volumes, and were of interest mostly to hobbyists and technicians. -
Abstractions for Programming Graphics Processors in High-Level Programming Languages
Abstracties voor het programmeren van grafische processoren in hoogniveau-programmeertalen Abstractions for Programming Graphics Processors in High-Level Programming Languages Tim Besard Promotor: prof. dr. ir. B. De Sutter Proefschrift ingediend tot het behalen van de graad van Doctor in de ingenieurswetenschappen: computerwetenschappen Vakgroep Elektronica en Informatiesystemen Voorzitter: prof. dr. ir. K. De Bosschere Faculteit Ingenieurswetenschappen en Architectuur Academiejaar 2018 - 2019 ISBN 978-94-6355-244-8 NUR 980 Wettelijk depot: D/2019/10.500/52 Examination Committee Prof. Filip De Turck, chair Department of Information Technology Faculty of Engineering and Architecture Ghent University Prof. Koen De Bosschere, secretary Department of Electronics and Information Systems Faculty of Engineering and Architecture Ghent University Prof. Bjorn De Sutter, supervisor Department of Electronics and Information Systems Faculty of Engineering and Architecture Ghent University Prof. Jutho Haegeman Department of Physics and Astronomy Faculty of Sciences Ghent University Prof. Jan Lemeire Department of Electronics and Informatics Faculty of Engineering Vrije Universiteit Brussel Prof. Christophe Dubach School of Informatics College of Science & Engineering The University of Edinburgh Prof. Alan Edelman Computer Science & Artificial Intelligence Laboratory Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology ii Dankwoord Ik wist eigenlijk niet waar ik aan begon, toen ik in 2012 in de cata- comben van het Technicum op gesprek ging over een doctoraat. Of ik al eens met LLVM gewerkt had. Ondertussen zijn we vele jaren verder, werk ik op een bureau waar er wel daglicht is, en is het eindpunt van deze studie zowaar in zicht. Dat mag natuurlijk wel, zo vertelt men mij, na 7 jaar. -
Python Guide Documentation 0.0.1
Python Guide Documentation 0.0.1 Kenneth Reitz 2015 11 07 Contents 1 3 1.1......................................................3 1.2 Python..................................................5 1.3 Mac OS XPython.............................................5 1.4 WindowsPython.............................................6 1.5 LinuxPython...............................................8 2 9 2.1......................................................9 2.2...................................................... 15 2.3...................................................... 24 2.4...................................................... 25 2.5...................................................... 27 2.6 Logging.................................................. 31 2.7...................................................... 34 2.8...................................................... 37 3 / 39 3.1...................................................... 39 3.2 Web................................................... 40 3.3 HTML.................................................. 47 3.4...................................................... 48 3.5 GUI.................................................... 49 3.6...................................................... 51 3.7...................................................... 52 3.8...................................................... 53 3.9...................................................... 58 3.10...................................................... 59 3.11...................................................... 62 -
Hyperlearn Documentation Release 1
HyperLearn Documentation Release 1 Daniel Han-Chen Jun 19, 2020 Contents 1 Example code 3 1.1 hyperlearn................................................3 1.1.1 hyperlearn package.......................................3 1.1.1.1 Submodules......................................3 1.1.1.2 hyperlearn.base module................................3 1.1.1.3 hyperlearn.linalg module...............................7 1.1.1.4 hyperlearn.utils module................................ 10 1.1.1.5 hyperlearn.random module.............................. 11 1.1.1.6 hyperlearn.exceptions module............................. 11 1.1.1.7 hyperlearn.multiprocessing module.......................... 11 1.1.1.8 hyperlearn.numba module............................... 11 1.1.1.9 hyperlearn.solvers module............................... 12 1.1.1.10 hyperlearn.stats module................................ 14 1.1.1.11 hyperlearn.big_data.base module........................... 15 1.1.1.12 hyperlearn.big_data.incremental module....................... 15 1.1.1.13 hyperlearn.big_data.lsmr module........................... 15 1.1.1.14 hyperlearn.big_data.randomized module....................... 16 1.1.1.15 hyperlearn.big_data.truncated module........................ 17 1.1.1.16 hyperlearn.decomposition.base module........................ 18 1.1.1.17 hyperlearn.decomposition.NMF module....................... 18 1.1.1.18 hyperlearn.decomposition.PCA module........................ 18 1.1.1.19 hyperlearn.decomposition.PCA module........................ 18 1.1.1.20 hyperlearn.discriminant_analysis.base -
Zmcintegral: a Package for Multi-Dimensional Monte Carlo Integration on Multi-Gpus
ZMCintegral: a Package for Multi-Dimensional Monte Carlo Integration on Multi-GPUs Hong-Zhong Wua,∗, Jun-Jie Zhanga,∗, Long-Gang Pangb,c, Qun Wanga aDepartment of Modern Physics, University of Science and Technology of China bPhysics Department, University of California, Berkeley, CA 94720, USA and cNuclear Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Abstract We have developed a Python package ZMCintegral for multi-dimensional Monte Carlo integration on multiple Graphics Processing Units(GPUs). The package employs a stratified sampling and heuristic tree search algorithm. We have built three versions of this package: one with Tensorflow and other two with Numba, and both support general user defined functions with a user- friendly interface. We have demonstrated that Tensorflow and Numba help inexperienced scientific researchers to parallelize their programs on multiple GPUs with little work. The precision and speed of our package is compared with that of VEGAS for two typical integrands, a 6-dimensional oscillating function and a 9-dimensional Gaussian function. The results show that the speed of ZMCintegral is comparable to that of the VEGAS with a given precision. For heavy calculations, the algorithm can be scaled on distributed clusters of GPUs. Keywords: Monte Carlo integration; Stratified sampling; Heuristic tree search; Tensorflow; Numba; Ray. PROGRAM SUMMARY Manuscript Title: ZMCintegral: a Package for Multi-Dimensional Monte Carlo Integration on Multi-GPUs arXiv:1902.07916v2 [physics.comp-ph] 2 Oct 2019 Authors: Hong-Zhong Wu; Jun-Jie Zhang; Long-Gang Pang; Qun Wang Program Title: ZMCintegral Journal Reference: ∗Both authors contributed equally to this manuscript. Preprint submitted to Computer Physics Communications October 3, 2019 Catalogue identifier: Licensing provisions: Apache License Version, 2.0(Apache-2.0) Programming language: Python Operating system: Linux Keywords: Monte Carlo integration; Stratified sampling; Heuristic tree search; Tensorflow; Numba; Ray.