Legate Numpy: Accelerated and Distributed Array Computing
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Sagemath and Sagemathcloud
Viviane Pons Ma^ıtrede conf´erence,Universit´eParis-Sud Orsay [email protected] { @PyViv SageMath and SageMathCloud Introduction SageMath SageMath is a free open source mathematics software I Created in 2005 by William Stein. I http://www.sagemath.org/ I Mission: Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab. Viviane Pons (U-PSud) SageMath and SageMathCloud October 19, 2016 2 / 7 SageMath Source and language I the main language of Sage is python (but there are many other source languages: cython, C, C++, fortran) I the source is distributed under the GPL licence. Viviane Pons (U-PSud) SageMath and SageMathCloud October 19, 2016 3 / 7 SageMath Sage and libraries One of the original purpose of Sage was to put together the many existent open source mathematics software programs: Atlas, GAP, GMP, Linbox, Maxima, MPFR, PARI/GP, NetworkX, NTL, Numpy/Scipy, Singular, Symmetrica,... Sage is all-inclusive: it installs all those libraries and gives you a common python-based interface to work on them. On top of it is the python / cython Sage library it-self. Viviane Pons (U-PSud) SageMath and SageMathCloud October 19, 2016 4 / 7 SageMath Sage and libraries I You can use a library explicitly: sage: n = gap(20062006) sage: type(n) <c l a s s 'sage. interfaces .gap.GapElement'> sage: n.Factors() [ 2, 17, 59, 73, 137 ] I But also, many of Sage computation are done through those libraries without necessarily telling you: sage: G = PermutationGroup([[(1,2,3),(4,5)],[(3,4)]]) sage : G . g a p () Group( [ (3,4), (1,2,3)(4,5) ] ) Viviane Pons (U-PSud) SageMath and SageMathCloud October 19, 2016 5 / 7 SageMath Development model Development model I Sage is developed by researchers for researchers: the original philosophy is to develop what you need for your research and share it with the community. -
KNIME Big Data Workshop
KNIME Big Data Workshop Björn Lohrmann KNIME © 2018 KNIME.com AG. All Rights Reserved. Variety, Velocity, Volume • Variety: – Integrating heterogeneous data… – ... and tools • Velocity: – Real time scoring of millions of records/sec – Continuous data streams – Distributed computation • Volume: – From small files... – ...to distributed data repositories – Moving computation to the data © 2018 KNIME.com AG. All Rights Reserved. 2 2 Variety © 2018 KNIME.com AG. All Rights Reserved. 3 The KNIME Analytics Platform: Open for Every Data, Tool, and User Data Scientist Business Analyst KNIME Analytics Platform External Native External Data Data Access, Analysis, and Legacy Connectors Visualization, and Reporting Tools Distributed / Cloud Execution © 2018 KNIME.com AG. All Rights Reserved. 4 Data Integration © 2018 KNIME.com AG. All Rights Reserved. 5 Integrating R and Python © 2018 KNIME.com AG. All Rights Reserved. 6 Modular Integrations © 2018 KNIME.com AG. All Rights Reserved. 7 Other Programming/Scripting Integrations © 2018 KNIME.com AG. All Rights Reserved. 8 Velocity © 2018 KNIME.com AG. All Rights Reserved. 9 Velocity • High Demand Scoring/Prediction: – Scoring using KNIME Server – Scoring with the KNIME Managed Scoring Service • Continuous Data Streams – Streaming in KNIME © 2018 KNIME.com AG. All Rights Reserved. 10 What is High Demand Scoring? • I have a workflow that takes data, applies an algorithm/model and returns a prediction. • I need to deploy that to hundreds or thousands of end users • I need to update the model/workflow periodically © 2018 KNIME.com AG. All Rights Reserved. 11 How to make a scoring workflow • Use JSON Input/Output nodes • Put workflow on KNIME Server -> REST endpoint for scoring © 2018 KNIME.com AG. -
Text Mining Course for KNIME Analytics Platform
Text Mining Course for KNIME Analytics Platform KNIME AG Copyright © 2018 KNIME AG Table of Contents 1. The Open Analytics Platform 2. The Text Processing Extension 3. Importing Text 4. Enrichment 5. Preprocessing 6. Transformation 7. Classification 8. Visualization 9. Clustering 10. Supplementary Workflows Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 2 Noncommercial-Share Alike license 1 https://creativecommons.org/licenses/by-nc-sa/4.0/ Overview KNIME Analytics Platform Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 3 Noncommercial-Share Alike license 1 https://creativecommons.org/licenses/by-nc-sa/4.0/ What is KNIME Analytics Platform? • A tool for data analysis, manipulation, visualization, and reporting • Based on the graphical programming paradigm • Provides a diverse array of extensions: • Text Mining • Network Mining • Cheminformatics • Many integrations, such as Java, R, Python, Weka, H2O, etc. Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 4 Noncommercial-Share Alike license 2 https://creativecommons.org/licenses/by-nc-sa/4.0/ Visual KNIME Workflows NODES perform tasks on data Not Configured Configured Outputs Inputs Executed Status Error Nodes are combined to create WORKFLOWS Licensed under a Creative Commons Attribution- ® Copyright © 2018 KNIME AG 5 Noncommercial-Share Alike license 3 https://creativecommons.org/licenses/by-nc-sa/4.0/ Data Access • Databases • MySQL, MS SQL Server, PostgreSQL • any JDBC (Oracle, DB2, …) • Files • CSV, txt -
Benchmarking the Intel FPGA SDK for Opencl Memory Interface
The Memory Controller Wall: Benchmarking the Intel FPGA SDK for OpenCL Memory Interface Hamid Reza Zohouri*†1, Satoshi Matsuoka*‡ *Tokyo Institute of Technology, †Edgecortix Inc. Japan, ‡RIKEN Center for Computational Science (R-CCS) {zohour.h.aa@m, matsu@is}.titech.ac.jp Abstract—Supported by their high power efficiency and efficiency on Intel FPGAs with different configurations recent advancements in High Level Synthesis (HLS), FPGAs are for input/output arrays, vector size, interleaving, kernel quickly finding their way into HPC and cloud systems. Large programming model, on-chip channels, operating amounts of work have been done so far on loop and area frequency, padding, and multiple types of blocking. optimizations for different applications on FPGAs using HLS. However, a comprehensive analysis of the behavior and • We outline one performance bug in Intel’s compiler, and efficiency of the memory controller of FPGAs is missing in multiple deficiencies in the memory controller, leading literature, which becomes even more crucial when the limited to significant loss of memory performance for typical memory bandwidth of modern FPGAs compared to their GPU applications. In some of these cases, we provide work- counterparts is taken into account. In this work, we will analyze arounds to improve the memory performance. the memory interface generated by Intel FPGA SDK for OpenCL with different configurations for input/output arrays, II. METHODOLOGY vector size, interleaving, kernel programming model, on-chip channels, operating frequency, padding, and multiple types of A. Memory Benchmark Suite overlapped blocking. Our results point to multiple shortcomings For our evaluation, we develop an open-source benchmark in the memory controller of Intel FPGAs, especially with respect suite called FPGAMemBench, available at https://github.com/ to memory access alignment, that can hinder the programmer’s zohourih/FPGAMemBench. -
How to Access Python for Doing Scientific Computing
How to access Python for doing scientific computing1 Hans Petter Langtangen1,2 1Center for Biomedical Computing, Simula Research Laboratory 2Department of Informatics, University of Oslo Mar 23, 2015 A comprehensive eco system for scientific computing with Python used to be quite a challenge to install on a computer, especially for newcomers. This problem is more or less solved today. There are several options for getting easy access to Python and the most important packages for scientific computations, so the biggest issue for a newcomer is to make a proper choice. An overview of the possibilities together with my own recommendations appears next. Contents 1 Required software2 2 Installing software on your laptop: Mac OS X and Windows3 3 Anaconda and Spyder4 3.1 Spyder on Mac............................4 3.2 Installation of additional packages.................5 3.3 Installing SciTools on Mac......................5 3.4 Installing SciTools on Windows...................5 4 VMWare Fusion virtual machine5 4.1 Installing Ubuntu...........................6 4.2 Installing software on Ubuntu....................7 4.3 File sharing..............................7 5 Dual boot on Windows8 6 Vagrant virtual machine9 1The material in this document is taken from a chapter in the book A Primer on Scientific Programming with Python, 4th edition, by the same author, published by Springer, 2014. 7 How to write and run a Python program9 7.1 The need for a text editor......................9 7.2 Spyder................................. 10 7.3 Text editors.............................. 10 7.4 Terminal windows.......................... 11 7.5 Using a plain text editor and a terminal window......... 12 8 The SageMathCloud and Wakari web services 12 8.1 Basic intro to SageMathCloud................... -
BCL: a Cross-Platform Distributed Data Structures Library
BCL: A Cross-Platform Distributed Data Structures Library Benjamin Brock, Aydın Buluç, Katherine Yelick University of California, Berkeley Lawrence Berkeley National Laboratory {brock,abuluc,yelick}@cs.berkeley.edu ABSTRACT high-performance computing, including several using the Parti- One-sided communication is a useful paradigm for irregular paral- tioned Global Address Space (PGAS) model: Titanium, UPC, Coarray lel applications, but most one-sided programming environments, Fortran, X10, and Chapel [9, 11, 12, 25, 29, 30]. These languages are including MPI’s one-sided interface and PGAS programming lan- especially well-suited to problems that require asynchronous one- guages, lack application-level libraries to support these applica- sided communication, or communication that takes place without tions. We present the Berkeley Container Library, a set of generic, a matching receive operation or outside of a global collective. How- cross-platform, high-performance data structures for irregular ap- ever, PGAS languages lack the kind of high level libraries that exist plications, including queues, hash tables, Bloom filters and more. in other popular programming environments. For example, high- BCL is written in C++ using an internal DSL called the BCL Core performance scientific simulations written in MPI can leverage a that provides one-sided communication primitives such as remote broad set of numerical libraries for dense or sparse matrices, or get and remote put operations. The BCL Core has backends for for structured, unstructured, or adaptive meshes. PGAS languages MPI, OpenSHMEM, GASNet-EX, and UPC++, allowing BCL data can sometimes use those numerical libraries, but are missing the structures to be used natively in programs written using any of data structures that are important in some of the most irregular these programming environments. -
An Introduction to Numpy and Scipy
An introduction to Numpy and Scipy Table of contents Table of contents ............................................................................................................................ 1 Overview ......................................................................................................................................... 2 Installation ...................................................................................................................................... 2 Other resources .............................................................................................................................. 2 Importing the NumPy module ........................................................................................................ 2 Arrays .............................................................................................................................................. 3 Other ways to create arrays............................................................................................................ 7 Array mathematics .......................................................................................................................... 8 Array iteration ............................................................................................................................... 10 Basic array operations .................................................................................................................. 11 Comparison operators and value testing .................................................................................... -
Advances, Applications and Performance of The
1 Introduction The two predominant classes of programming models for MIMD concurrent computing are distributed memory and ADVANCES, APPLICATIONS AND shared memory. Both shared memory and distributed mem- PERFORMANCE OF THE GLOBAL ory models have advantages and shortcomings. Shared ARRAYS SHARED MEMORY memory model is much easier to use but it ignores data PROGRAMMING TOOLKIT locality/placement. Given the hierarchical nature of the memory subsystems in modern computers this character- istic can have a negative impact on performance and scal- Jarek Nieplocha1 1 ability. Careful code restructuring to increase data reuse Bruce Palmer and replacing fine grain load/stores with block access to Vinod Tipparaju1 1 shared data can address the problem and yield perform- Manojkumar Krishnan ance for shared memory that is competitive with mes- Harold Trease1 2 sage-passing (Shan and Singh 2000). However, this Edoardo Aprà performance comes at the cost of compromising the ease of use that the shared memory model advertises. Distrib- uted memory models, such as message-passing or one- Abstract sided communication, offer performance and scalability This paper describes capabilities, evolution, performance, but they are difficult to program. and applications of the Global Arrays (GA) toolkit. GA was The Global Arrays toolkit (Nieplocha, Harrison, and created to provide application programmers with an inter- Littlefield 1994, 1996; Nieplocha et al. 2002a) attempts to face that allows them to distribute data while maintaining offer the best features of both models. It implements a the type of global index space and programming syntax shared-memory programming model in which data local- similar to that available when programming on a single ity is managed by the programmer. -
Sage for Lattice-Based Cryptography
Sage for Lattice-based Cryptography Martin R. Albrecht and Léo Ducas Oxford Lattice School Outline Sage Lattices Rings Sage Blurb Sage open-source mathematical software system “Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.” Sage is a free open-source mathematics software system licensed under the GPL. It combines the power of many existing open-source packages into a common Python-based interface. How to use it command line run sage local webapp run sage -notebook=jupyter hosted webapp https://cloud.sagemath.com 1 widget http://sagecell.sagemath.org 1On SMC you have the choice between “Sage Worksheet” and “Jupyter Notebook”. We recommend the latter. Python & Cython Sage does not come with yet-another ad-hoc mathematical programming language, it uses Python instead. • one of the most widely used programming languages (Google, IML, NASA, Dropbox), • easy for you to define your own data types and methods on it (bitstreams, lattices, cyclotomic rings, :::), • very clean language that results in easy to read code, • a huge number of libraries: statistics, networking, databases, bioinformatic, physics, video games, 3d graphics, numerical computation (SciPy), and pure mathematic • easy to use existing C/C++ libraries from Python (via Cython) Sage =6 Python Sage Python 1/2 1/2 1/2 0 2^3 2^3 8 1 type(2) type(2) <type 'sage.rings.integer.Integer'> <type 'int'> Sage =6 Python Sage Python type(2r) type(2r) <type 'int'> SyntaxError: invalid syntax type(range(10)[0]) type(range(10)[0]) <type 'int'> <type 'int'> -
Homework 2 an Introduction to Convolutional Neural Networks
Homework 2 An Introduction to Convolutional Neural Networks 11-785: Introduction to Deep Learning (Spring 2019) OUT: February 17, 2019 DUE: March 10, 2019, 11:59 PM Start Here • Collaboration policy: { You are expected to comply with the University Policy on Academic Integrity and Plagiarism. { You are allowed to talk with / work with other students on homework assignments { You can share ideas but not code, you must submit your own code. All submitted code will be compared against all code submitted this semester and in previous semesters using MOSS. • Overview: { Part 1: All of the problems in Part 1 will be graded on Autolab. You can download the starter code from Autolab as well. This assignment has 100 points total. { Part 2: This section of the homework is an open ended competition hosted on Kaggle.com, a popular service for hosting predictive modeling and data analytic competitions. All of the details for completing Part 2 can be found on the competition page. • Submission: { Part 1: The compressed handout folder hosted on Autolab contains four python files, layers.py, cnn.py, mlp.py and local grader.py, and some folders data, autograde and weights. File layers.py contains common layers in convolutional neural networks. File cnn.py contains outline class of two convolutional neural networks. File mlp.py contains a basic MLP network. File local grader.py is foryou to evaluate your own code before submitting online. Folders contain some data to be used for section 1.3 and 1.4 of this homework. Make sure that all class and function definitions originally specified (as well as class attributes and methods) in the two files layers.py and cnn.py are fully implemented to the specification provided in this write-up. -
Enabling Efficient Use of UPC and Openshmem PGAS Models on GPU Clusters
Enabling Efficient Use of UPC and OpenSHMEM PGAS Models on GPU Clusters Presented at GTC ’15 Presented by Dhabaleswar K. (DK) Panda The Ohio State University E-mail: [email protected] hCp://www.cse.ohio-state.edu/~panda Accelerator Era GTC ’15 • Accelerators are becominG common in hiGh-end system architectures Top 100 – Nov 2014 (28% use Accelerators) 57% use NVIDIA GPUs 57% 28% • IncreasinG number of workloads are beinG ported to take advantage of NVIDIA GPUs • As they scale to larGe GPU clusters with hiGh compute density – hiGher the synchronizaon and communicaon overheads – hiGher the penalty • CriPcal to minimize these overheads to achieve maximum performance 3 Parallel ProGramminG Models Overview GTC ’15 P1 P2 P3 P1 P2 P3 P1 P2 P3 LoGical shared memory Shared Memory Memory Memory Memory Memory Memory Memory Shared Memory Model Distributed Memory Model ParPPoned Global Address Space (PGAS) DSM MPI (Message PassinG Interface) Global Arrays, UPC, Chapel, X10, CAF, … • ProGramminG models provide abstract machine models • Models can be mapped on different types of systems - e.G. Distributed Shared Memory (DSM), MPI within a node, etc. • Each model has strenGths and drawbacks - suite different problems or applicaons 4 Outline GTC ’15 • Overview of PGAS models (UPC and OpenSHMEM) • Limitaons in PGAS models for GPU compuPnG • Proposed DesiGns and Alternaves • Performance Evaluaon • ExploiPnG GPUDirect RDMA 5 ParPPoned Global Address Space (PGAS) Models GTC ’15 • PGAS models, an aracPve alternave to tradiPonal message passinG - Simple -
Automatic Handling of Global Variables for Multi-Threaded MPI Programs
Automatic Handling of Global Variables for Multi-threaded MPI Programs Gengbin Zheng, Stas Negara, Celso L. Mendes, Laxmikant V. Kale´ Eduardo R. Rodrigues Department of Computer Science Institute of Informatics University of Illinois at Urbana-Champaign Federal University of Rio Grande do Sul Urbana, IL 61801, USA Porto Alegre, Brazil fgzheng,snegara2,cmendes,[email protected] [email protected] Abstract— necessary to privatize global and static variables to ensure Hybrid programming models, such as MPI combined with the thread-safety of an application. threads, are one of the most efficient ways to write parallel ap- In high-performance computing, one way to exploit multi- plications for current machines comprising multi-socket/multi- core nodes and an interconnection network. Global variables in core platforms is to adopt hybrid programming models that legacy MPI applications, however, present a challenge because combine MPI with threads, where different programming they may be accessed by multiple MPI threads simultaneously. models are used to address issues such as multiple threads Thus, transforming legacy MPI applications to be thread-safe per core, decreasing amount of memory per core, load in order to exploit multi-core architectures requires proper imbalance, etc. When porting legacy MPI applications to handling of global variables. In this paper, we present three approaches to eliminate these hybrid models that involve multiple threads, thread- global variables to ensure thread-safety for an MPI program. safety of the applications needs to be addressed again. These approaches include: (a) a compiler-based refactoring Global variables cause no problem with traditional MPI technique, using a Photran-based tool as an example, which implementations, since each process image contains a sep- automates the source-to-source transformation for programs arate instance of the variable.