CENG 505 Parallel Computing I
Fall 2006

Most recent announcement: Jan26

Announcements

Watch this space for the latest updates. Last updated: 26.Ocak.2007 15:19 Term projects are accesible.

22.Ocak.2007 16:51 The project presentations will be on Jan 25, 2007 13.00 PM at A-319.

January 4, 2007 13:31 Project Topics:

• Serkan Kefel :Parallel Data Compression

• Serdar Taşel: Parallel Implementation of Fermat's factorization method

• Pelin Guvenc: Parallel Harris Corner Detection

• Burcak Sonmez: Parallel Edge Detection

• Anil Sarpkaya: Parallel Password Cracker

• Mete Bulutay: Parallel Encryption Algorithms

• Umit Atas: Parallel Search Algorithms

December 27, 2006 14:58 The lecture notes for the fourteenth week is published, see Course Schedule. Project Topics:

December 20, 2006 19:52 Project Topics:

December 20, 2006 13:54 The lecture notes and Hands-On for the thirteenth week and Hands-On for the fourteenth week is published, see Course Schedule

December 15, 2006 19:11 Project Topics:

December 13, 2006 17:05The lecture notes and Hands-On for the twelfth week is published, see Course Schedule

December 6, 2006 16:41 The lecture notes and Hands-On for the eleventh week is published, see Course Schedule

November 29, 2006 16:20The lecture notes and Hands-On for the tenth week is published, see Course Schedule

November 15, 2006 19:27 The lecture notes and Hands-On for the nineth week is published, see Course Schedule

November 8, 2006 16:48 The lecture notes and Hands-On for the seventh week is published, see Course Schedule

November 3, 2006 18:54 Lecture and Office Hours are rearranged, see the time table above.

November 1, 2006 16:27 The lecture notes and Hands-On for the sixth week is published, see Course Schedule

October 23, 2006 22:51 The lecture notes for the fifth week is published, see Course Schedule

October 20, 2006 14:17 The Hands-On for the fourth week is published, see Course Schedule

October 19, 2006 02:19 The lecture notes for the fourth week is published, see Course Schedule

October 13, 2006 14:10 The Hands-On for the third week is published, see Course Schedule

October 12, 2006 18:23 The lecture notes for the third week is published, see Course Schedule

October 6, 2006 17:45 The lecture notes for the second week and also the Hands-Ons are published, see Course Schedule

September 28, 2006 09:38 In the first lecture, there will be first metting. The lecture notes for the second week will be published soon, see Course Schedule section.

Overview

This course provides an introduction to parallel and distributed computing and practical experiences in writing parallel programs on a cluster of computers. You will learn about the following topics:

• Parallel Computers

• Message Passing Computing

• Embarrassingly Parallel Computations

• Partitioning and Divide-and-Conquer Strategies

• Pipelined Computations

• Synchronous Computations

• Load Balancing

• Programming with Shared Memory

Topics might be classifed into two main parts as;

• Parallel computers: architectural types, shared memory, message passing, interconnection networks, potential for increased speed.

• Basic techniques: embarrassingly parallel computations, partitioning and divide and conquer, pipelined computations, synchronous computations, load balancing, shared memory programming.

Lecture Information

There is one group for lecturing. You will be expected to do significant programming assignments, as well as run programs we supply and analyze the output. Since we will program in C on a UNIX environment, some experience using C on UNIX will be important. We will provide tutorials for basic C on UNIX during the first few class periods.

In hands-on sessions, we will concentrate upon the message-passing method of parallel computing and use the standard parallel computing environment called MPI (Message Passing Interface). Thread-based programming will also be outlined, and the distributed shared memory (DSM) approach (If we have enough time). Each student will complete a project based on parallel computing for the laboratory study.

Also, each student will complete a project based on parallel computing, (distributed computing, cluster computing) for the midterm exam.

Important announcements will be posted to the Announcements section of this web page above, so please check this page frequently. You are responsible for all such announcements, as well as announcements made in lecture.

Course Outline

• Contents

• List of Tables

• List of Figures

• Introduction

  • Four Decades of Computing

  • Flynn's Taxonomy of Computer Architecture

  • SIMD Architecture

  • MIMD Architecture

    • Shared Memory Organization

    • Message Passing Organization

  • Interconnection Networks

  • Introduction to MPI

    • Parallel Computing

    • Types of parallel computing

    • Communicating with other processes

    • Hardware models

    • What is MPI?

    • Who Designed MPI?

    • MPI Implementations

    • Is MPI Large or Small?

    • Where to use MPI?

    • How To Use MPI?

    • Getting started

      • Writing MPI programs

      • Compiling and linking

      • Running MPI programs

      • Finding out about the environment

      • A simple program

      • Exercise - Getting Started

• Multiprocessors Interconnection Networks

  • Interconnection Networks Taxonomy

  • Bus-based Dynamic Interconnection Networks

    • Single Bus Systems

    • Multiple Bus Systems

    • Bus Synchronization

  • Switch-Based Interconnection Networks

    • Crossbar Networks

    • Single-Stage Networks

    • Multistage Networks

    • Blockage in Multistage Interconnection Networks

  • Static Interconnection Networks

    • Completely Connected Networks

    • Limited Connection Networks

  • Analysis and Performance Metrics

    • Dynamic Networks

    • Static Networks

  • Sending and Receiving messages

    • Current Message-Passing

    • The Buffer

    • Sample Program using Library Calls

    • MPI Basic Send/Receive

    • Exercise/Example: Translate this Fortran http://siber.cankaya.edu.tr/ParallelComputing/cfiles/sendreceive.fcode to C

    • Computation of PI as an example

    • Exercise

  • MPI Hands-On; Examples

• Performance Analysis

  • Computational Models

    • Equal Duration Model

    • Parallel Computation with Serial Sections Model

  • Skeptic Postulates For Parallel Architectures

    • Grosch's Law

    • Amdahl's Law

    • Gustafson-Barsis's Law

  • Scalability of Parallel Architectures

  • Assignment:

  • Performance tuning MPI 1

• Shared Memory Architecture

  • Classification of Shared Memory Systems

    • Uniform Memory Access (UMA)

    • Nonuniform Memory Access (NUMA)

    • Cache-Only Memory Architecture (COMA)

  • Bus-based Symmetric Multiprocessors

  • Basic Cache Coherency Methods

    • Cache-Memory Coherence

    • Cache-Cache Coherence

    • Shared Memory System Coherence

  • Shared Memory Programming

    • Task Creation

    • Communication

    • Synchronization

    • Thread Basics

  • Performance tuning MPI 2

• Programming Shared Memory

  • Why Threads?

  • Thread Basics: Creation and Termination

  • Synchronization Primitives in Pthreads

    • Mutual Exclusion for Shared Variables

  • Shared Memory I; Processes, Threads

    • Condition Variables for Synchronization

  • Controlling Thread and Synchronization Attributes

    • Attributes Objects for Threads

  • Thread Cancellation

  • Composite Synchronization Constructs

    • Barriers

  • Tips for Designing Asynchronous Programs

  • OpenMP: a Standard for Directive Based Parallel Programming

    • The OpenMP Programming Model

  • Assignment:

  • Shared Memory II; Threads, OpenMP Examples

• Message Passing Architecture

  • Introduction to Message Passing

  • Routing in Message Passing Networks

    • Routing for Broadcasting and Multicasting

    • Routing Potential Problems

  • Switching Mechanisms in Message Passing

  • Processor Support for Message Passing

  • Example Message Passing Architectures

  • Message Passing vs Shared Memory

  • Parallel Summation

• Programming Using the Message-Passing Paradigm

  • Principles of Message-Passing Programming

    • Structure of Message-Passing Programs

  • The Building Blocks: Send and Receive Operations

    • Blocking Message Passing Operations

    • Non-Blocking Message Passing Operations

  • MPI: the Message Passing Interface

    • Starting and Terminating the MPI Library

    • Communicators

    • Getting Information

    • Sending and Receiving Messages

  • Examples; Buffer Limit, Barrier, Collective Communications.

  • Overlapping Communication with Computation

    • Non-Blocking Communication Operations

  • Collective Communication and Computation Operations

    • Reduction

    • Gather

    • Scatter

    • All-to-All

  • Groups and Communicators

  • Examples; Non-blocking Communications and Parallel Matrix Multiplication.

• Introduction to Parallel Algorithms

  • Odd-Even Sort

  • Cannon's Matrix-Matrix Multiplication with MPI's Topologies

  • One-Dimensional Matrix-Vector Multiplication

  • Two-Dimensional Matrix-Vector Multiplication

  • Examples; Parallel Algorithms

  • Network Computing

  • Computer Networks Basics

    • Network Performance

    • Internet

    • Other Network Technologies

  • Client/Server Systems

    • Sockets

    • Remote Procedure Call (RPC)

    • Middleware

    • A Client Server Framework for Parallel Applications

  • Clusters

    • Threads

  • Interconnection Networks

    • Ethernet

    • Switches

  • Myrinet Clos Network

    • The Quadrics Network

  • Cluster Examples

    • Berkeley Network of Workstations (NOW)

    • The Beowulf Cluster

    • FlashMob I

  • Grid Computing

• References:

• vita

• About this document ...

Text Book

Required

Recommended

• Readings will be assigned in Parallel Programming: Techniques and Application Using Networked Workstations and Parallel Computers, 2^nd edition, by B. Wilkinson and M. Allen, Prentice Hall Inc., 2005, ISBN 0-13-140563-2.

• Beowulf Cluster Computing with Linux, 2nd edition, edited by William Gropp, Ewing Lusk, Thomas Sterling, MIT Press, 2003, ISBN 0-262-69292-9.

• Beowulf Cluster Computing with Windows, Thomas Sterling , MIT Press, 2001, ISBN 0-262-69275-9.

• Using MPI , Portable Parallel Programming with the Message Passing Interface, William Gropp, Ewing Lusk and Anthony Skjellum, The MIT Press, 1999, ISBN 0-262-57132-3.

• Using MPI-2, Advanced Features of the Message Passing Interface, William Gropp, Ewing Lusk, Rajeev Thakur, The MIT Press, 1999, ISBN 0-262-57133-1.

• MPI: The Complete Reference (Vol. 1) - The MPI Core, Marc Snir, Steve Otto, Steven Huss-Lederman, David Walker and Jack Dongarra, The MIT Press, 1998, ISBN 0-262-69215-5.

• MPI: The Complete Reference (Vol. 2) - The MPI-2 Extensions, William Gropp, Steven Huss-Lederman, Andrew Lumsdaine, Ewing Lusk, Bill Nitzberg, William Saphir and Marc Snir, The MIT Press, 1998, ISBN 0-262-57123-4.

• In Search of Clusters: The ongoing battle in lowly parallel computing, Second Edition, by Gregory F. Pfister, Prentice Hall Publishing Company, 1998, ISBN: 0-13-899709-8.

• How to Build a Beowulf – A Guide to the Implementation and Application of PC Clusters, by Thomas Sterling, John Salmon, Donald J. Becker and Daniel F. Savarese, MIT Press, 1999, ISBN 0-262-69218-X.

• PVM: Parallel Virtual Machine, A Users' Guide and Tutorial for Network Parallel Computing, Al Geist, Adam Beguelin, Jack Dongarra, Weicheng Jiang, Robert Manchek and Vaidyalingam S. Sunderam, MIT Press, 1994, ISBN 0-262-57108-0.

This texts are only recommended rather than required. This books are useful for reference, for an alternative point of view.

Online References

Some materials are given. Please inform me about the usefullness of the materials. Check this place for updates.

The following references are available online

• Take a look at the TOP500 list

• MPI: The Complete Reference

• Message Passing Interface Forum

• MPICH Home Page

• MPI Man pages (Web format)

• ANSI C for Programmers on UNIX Systems

• Greg Wilson's Parallel Computing Timeline (1955 to 1993)

• I. Foster. Designing and Building Parallel Programs, Addison-Wesley, 1995 available on-line

• Glossary of Terms

Grading Criteria

• There will be a final exam: 40%

• Term Project as Midterm exam: 25%

• Term Project as Lab. exam: 25%

• Attendance is required and constitutes part of your course grade; 10%

Policies

• Attendance is not compulsory, but you are responsible for everything said in class.

• I encourage you to ask questions in class. You are supposed to ask questions. Don't guess, ask a question!

• You may discuss homework problems with classmates (although it is not to your advantage to do so).

• You can use ideas from the literature (with proper citation).

• You can use anything from the textbook/notes.

• The code you submit must be written completely by you.

Course Schedule

The following schedule is tentative; it may be updated later in the semester, so check back here frequently.