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Mastering Parallel Programming with R
Mastering Parallel Programming with R

Mastering Parallel Programming with R: Master the robust features of R parallel programming to accelerate your data science computations

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Profile Icon Simon R. Chapple Profile Icon Sloan Profile Icon Forster Profile Icon Troup
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Paperback May 2016 244 pages 1st Edition
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Arrow left icon
Profile Icon Simon R. Chapple Profile Icon Sloan Profile Icon Forster Profile Icon Troup
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Paperback May 2016 244 pages 1st Edition
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Mastering Parallel Programming with R

Chapter 2. Introduction to Message Passing

In this chapter, we will take our first look at a lower level of parallelism: explicit message passing between multiple communicating R processes. We will utilize the standard Message Passing Interface (MPI) API available to us in a number of forms on laptops, cloud clusters, and supercomputers.

In this chapter, you will learn about:

  • The MPI API and how to use this via the two different R packages, Rmpi and pbdMPI, together with the OpenMPI implementation of the communications subsystem
  • Blocking and non-blocking point-to-point communications
  • Group-based collective communications

In the next two chapters, we will explore a more advanced use of MPI, including grid-based parallel processing and running R to scale on a real-life supercomputer; however, for now, we will take an introductory tour of MPI and once again focus on our own Mac computer as the target compute environment; the information required to get you up and running with MPI on Microsoft...

Setting up your system environment for MPI

In order to use MPI with R, there are a number of prerequisites we need to install. The picture is a little more complicated for setting up MPI as compared to other R packages as we require both an R interface to MPI and an implementation of MPI that it will call into. We also have a number of options available to us, both for the R package and for the underlying MPI subsystem.

Choice of R packages for MPI

There are two MPI-based R-interfacing packages available that we can make use of, namely Rmpi and pbdMPI:

Note

Rmpi is available from CRAN at the following link: https://cran.r-project.org/web/packages/Rmpi/index.html

The main Rmpi website is http://www.stats.uwo.ca/faculty/yu/Rmpi/.

Instructions for installing Rmpi on Mac OS X are provided at http://www.stats.uwo.ca/faculty/yu/Rmpi/mac_os_x.htm.

Instructions for installing Rmpi on Windows are provided at http://www.stats.uwo.ca/faculty/yu/Rmpi/windows.htm.

The pbdMPI package is available from CRAN...

The MPI standard

You can view the complete version 3.0 MPI standard, which runs to a desk-walloping 822 pages in the form of a PDF Report at (MPI Ref) http://www.mpi-forum.org/docs/mpi-3.0/mpi30-report.pdf.

At the time of writing, version 3.1 of the MPI standard is published (June 2015). Although we will be focusing on the previous version, that is 3.0, the differences are not material for our purposes. MPI version 3.0 is both mature and comprehensive.

Due to some of the limitations of R and, in particular, its inherent single-threaded nature, only a subset of the MPI standard is implemented in either Rmpi or pbdMPI. However, all the basics for point-to-point and collective group communications are available, and we shall explore these through the remainder of this chapter. To begin, we need to understand some basic concepts that apply to the world of MPI.

The MPI universe

MPI considers each separate thread of computation to be a process, and each process is assigned a unique rank, which is...

The MPI API

We will divide our coverage of the MPI API into two: firstly, point-to-point communications followed by group-wise collective communications. Additional functionality beyond the core communication is described later in the advanced MPI API section.

First however, we need to explain some differences in the approaches to parallelism adopted by Rmpi and pbdMPI. We have already discussed that Rmpi can run within an interactive R session, whereas the pbdMPI R programs can only be run using mpiexec from a command shell (Rmpi programs can also be run with mpiexec).

Rmpi adopts the master/worker paradigm and dynamically launches worker processes internally using MPI_Comm_spawn(), where the launching R session is the master and the workers form the computational cluster. Code blocks that may include MPI communication are then issued by the master for remote execution by the worker cluster, which each execute an Rmpi daemon-style R script actively waiting for the next command to be broadcast...

Summary

Right, it's time to take a wee breather. In this chapter, we covered the basic concepts and the API for MPI. You learned how to utilize both the Rmpi and pbdMPI packages in conjunction with OpenMPI. We explored a number of simple examples of both blocking and non-blocking communications in R and also introduced the collective communications operations in MPI. We looked into the low-level implementation of Rmpi package's own master/worker scheme to manage the execution of R code in parallel. You now have sufficient grounding to write a wide variety of highly scalable MPI programs in R.

In the next chapter, we will complete our discussion on MPI, work through a particular MPI example that introduces spatial grid-style parallelism, and cover the remaining slightly more esoteric MPI API functions available to us in R.

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Key benefits

  • *Create R programs that exploit the computational capability of your cloud platforms and computers to the fullest
  • *Become an expert in writing the most efficient and highest performance parallel algorithms in R
  • *Get to grips with the concept of parallelism to accelerate your existing R programs

Description

R is one of the most popular programming languages used in data science. Applying R to big data and complex analytic tasks requires the harnessing of scalable compute resources. Mastering Parallel Programming with R presents a comprehensive and practical treatise on how to build highly scalable and efficient algorithms in R. It will teach you a variety of parallelization techniques, from simple use of R’s built-in parallel package versions of lapply(), to high-level AWS cloud-based Hadoop and Apache Spark frameworks. It will also teach you low level scalable parallel programming using RMPI and pbdMPI for message passing, applicable to clusters and supercomputers, and how to exploit thousand-fold simple processor GPUs through ROpenCL. By the end of the book, you will understand the factors that influence parallel efficiency, including assessing code performance and implementing load balancing; pitfalls to avoid, including deadlock and numerical instability issues; how to structure your code and data for the most appropriate type of parallelism for your problem domain; and how to extract the maximum performance from your R code running on a variety of computer systems.

Who is this book for?

This book is for R programmers who want to step beyond its inherent single-threaded and restricted memory limitations and learn how to implement highly accelerated and scalable algorithms that are a necessity for the performant processing of Big Data. No previous knowledge of parallelism is required. This book also provides for the more advanced technical programmer seeking to go beyond high level parallel frameworks.

What you will learn

  • *Create and structure efficient load-balanced parallel computation in R, using R's built-in parallel package
  • *Deploy and utilize cloud-based parallel infrastructure from R, including launching a distributed computation on Hadoop running on Amazon Web Services (AWS)
  • *Get accustomed to parallel efficiency, and apply simple techniques to benchmark, measure speed and target improvement in your own code
  • *Develop complex parallel processing algorithms with the standard Message Passing Interface (MPI) using RMPI, pbdMPI, and SPRINT packages
  • *Build and extend a parallel R package (SPRINT) with your own MPI-based routines
  • *Implement accelerated numerical functions in R utilizing the vector processing capability of your Graphics Processing Unit (GPU) with OpenCL
  • *Understand parallel programming pitfalls, such as deadlock and numerical instability, and the approaches to handle and avoid them
  • *Build a task farm master-worker, spatial grid, and hybrid parallel R programs
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Table of Contents

7 Chapters
1. Simple Parallelism with R Chevron down icon Chevron up icon
2. Introduction to Message Passing Chevron down icon Chevron up icon
3. Advanced Message Passing Chevron down icon Chevron up icon
4. Developing SPRINT, an MPI-Based R Package for Supercomputers Chevron down icon Chevron up icon
5. The Supercomputer in Your Laptop Chevron down icon Chevron up icon
6. The Art of Parallel Programming Chevron down icon Chevron up icon
Index Chevron down icon Chevron up icon

Customer reviews

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Full star icon Full star icon Full star icon Full star icon Full star icon 5
(4 Ratings)
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Richard Seitz Jan 04, 2019
Full star icon Full star icon Full star icon Full star icon Full star icon 5
Ich hatte bisher nur Grundlegende Kenntnisse.Da ich nun für div. Auswertungen auf R aufbauen wollte und viel Wert auf Performance lege, habe ich mir dieses Buch zugelegt.Es ist alles was man für paralleles Programmieren benötigt gut und ausführlich beschrieben.Gerade für mich als Anfänger war das Buch sehr hilfreich und ich habe einen Performancegewinn von über 200 % erziehlt.Kann das Buch deshalb guten Gewissens weiter empfehlen.
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Steven P. Sanderson Jun 23, 2016
Full star icon Full star icon Full star icon Full star icon Full star icon 5
This book gives nice clear concise examples of how to perform parallel programming in R. There are many great examples to follow that help you get an understanding of how this paradigm of programming does and does not work. The author understands that the material can be difficult to grasp but gives a clear explanation that will sink in with readers. He discusses the pro's and the con's of parallel programming, where it is beneficial and where it is not. For anyone wanting to obtain an understanding of parallel programming inside of R, I would recommend this book.
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Sven-Ivar Fjeld Nov 05, 2016
Full star icon Full star icon Full star icon Full star icon Full star icon 5
My knowledge of parallel computing is, in other languages, decent. It was therefore great to read this book which introduced me to the R ways of doing things in a parallel fashion, along with some great custom functions, examples, and solutions. As a personal example of how this book benefitted me, I was able to reduce the time taken by a particular computational heavy asset allocation algorithm of mine from an average of 4.6 mins to 2.3 mins. Looking forward to how this can be brought down further with the use of GPUs and other interesting methods.
Amazon Verified review Amazon
Sven-Ivar Fjeld Nov 05, 2016
Full star icon Full star icon Full star icon Full star icon Full star icon 5
My knowledge of parallel computing is, in other languages, decent. It was therefore great to read this book which introduced me to the R ways of doing things in a parallel fashion, along with some great custom functions, examples, and solutions. As a personal example of how this book benefitted me, I was able to reduce the time taken by a particular computational heavy asset allocation algorithm of mine from an average of 4.6 mins to 2.3 mins. Looking forward to how this can be brought down further with the use of GPUs and other interesting methods.
Amazon Verified review Amazon
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