Book Image

Mastering Parallel Programming with R

By : Simon R. Chapple, Terence Sloan, Thorsten Forster, Eilidh Troup
Book Image

Mastering Parallel Programming with R

By: Simon R. Chapple, Terence Sloan, Thorsten Forster, Eilidh Troup

Overview of this book

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.
Table of Contents (13 chapters)

Chapter 4. Developing SPRINT, an MPI-Based R Package for Supercomputers

In this chapter, we will learn how to use a form of parallelism called message passing, written in the widely adopted Message Passing Interface (MPI) standard, and how to utilize MPI-based parallel routines written in other programming languages directly from an R script.

We will start with a simple "Hello World" MPI program, and transform it into an R library package. This will demonstrate how you can take an existing MPI code written in C and make it directly callable from R.

We will then delve into the architecture of an MPI-based R package, commonly known as Simple Parallel R Interface (SPRINT). SPRINT provides a suite of MPI-parallel routines of particular use to bio-informaticians and life scientists for genomic analysis. We will show how you can further extend its utility by adding your own parallel functionality to the package.

Finally, we will explore the performance characteristics of a SPRINT-based genomics analysis...