paper/paper.md

In prdm0/ropenblas: Download, Compile and Link 'OpenBLAS' Library with R

Example from https://joss.readthedocs.io/en/latest/submitting.html

title: 'ropenblas: Download, Compile and Link OpenBLAS Library with R' tags: - R - Compiling R and OpenBLAS - Link OpenBLAS - Switch between versions of R - Fast algebraic computing authors: - name: Pedro Rafael Diniz Marinho orcid: 0000-0003-1591-8300 affiliation: 1 affiliations: - name: Department of Statistics, Federal University of Paraíba, João Pessoa, Paraíba - PB, Brazil index: 1 citation_author: Marinho date: "2021-03-30" year: "2021" bibliography: paper.bib output: rticles::joss_article header-includes: - \usepackage{float} csl: apa.csl journal: JOSS

Summary

The ropenblas package provides improved performance on GNU/Linux systems and allows for passing additional compilation flags for more technical users. Through the ropenblas() and rcompiler() functions, the user will be able to compile and link the GNU/Linux distribution R language with the OpenBLAS library, all within R and in a very simple fashion. It works for all GNU/Linux distributions. Linking the OpenBLAS library to R brings better computational performance to the language in the most diverse algebraic operations commonly used in areas such as statistics, data science, and machine learning.

Introduction

Computational efficiency is important for those who program statistical methods since they often involve algebraic operations reproduced in computationally intensive simulations, such as Monte-Carlo simulations and resampling methods, as is the case with bootstrap resampling. Statistics is just one example within other areas that need good performance and use the R language.

In addition to the adoption of good programming practices and the maximum, efficient and adequate use of available computational resources, such as code parallelization, through multicore parallelism procedures allowed by most current processors and operating systems, small adjustments and linkage of libraries can provide useful benefits.

The ropenblas package aims to be easy to use for R [@R] programmers who work on GNU/Linux operating systems. For example, a user can link any version of the OpenBLAS [@openblas] library to the R language and install and link various versions of R to make them available on their operating system as well as switch between these versions.

Linking the R language to the OpenBLAS library can bring several benefits to algebraic computing in R. OpenBLAS is an Open-Source implementation of the Basic Linear Algebra Subprograms - BLAS library that is often the first library option for algebraic computing to be linked in the installation of R on many GNU/Linux distributions. The OpenBLAS library is available at https://github.com/xianyi/OpenBLAS and adds optimized implementations of linear algebra kernels that can run optimized on various processor architectures. OpenBLAS is based on the GotoBLAS2 project code in version 1.13 [@gotoblas2], code available under the terms of the BSD license.

The ropenblas is a package designed to facilitate the linking of the library OpenBLAS with the language R. The package, which works only for Linux systems, will automatically download the latest source code from the OpenBLAS library and compile the code. The package will automatically bind the language R, through the ropenblas() function, to use the OpenBLAS library. Everything will be done automatically regardless of the Linux distribution you are using. Enumerating some advantages of the package:

1. Everything is done within the R language;
2. The procedure (use of functions) will be the same for any Linux distribution;
3. The OpenBLAS library will be compiled and you will choose which build version to bind to R, regardless of your Linux distribution;
4. The package allows you to install R $\geq 3.1.0$, also allowing you to install one more version, in addition to allowing you to easily switch between those versions;
5. The linked versions of R will continue to be recognized by their Integrated Development Environment - IDE and nothing will have to be adjusted in your GNU/Linux distribution after using any function of the package;
6. Unnecessary builds will be avoided. Therefore, if you need to switch between compiled versions of the R language, the use of binaries compiled compiled previously will be suggested;
7. If any errors occur, the functions of the package will not damage the previous installation of the language;
8. If something better can be done or if a newer version of what you want to install (R or OpenBLAS) exists, the functions will automatically suggest that you should consider installing newer versions.

The ropenblas package is already available on the Comprehensive R Archive Network - CRAN, currently in version 0.2.9, and the project is maintained on GitHub at https://github.com/prdm0/ropenblas where contributors can find other details of the code, information, as well as being able to contribute with the development of the project. On the website, it is also possible to read the NEWS.md file with details of the versions and the focus of the current development. The site is deposited at https://prdm0.github.io/ropenblas/. Suggestions for improvements and bug reports can be sent via the link https://github.com/prdm0/ropenblas/issues. You can find out how to contribute to the package by accessing the CONTRIBUTING.md file at https://github.com/prdm0/ropenblas/blob/master/CONTRIBUTING.md.

\begin{figure}[H]

{\centering \includegraphics[width=0.3\linewidth]{logo}

}

\caption{Computer library logo.}\label{fig:logo} \end{figure}

Brief explanation

The ropenblas library exports six functions for use which are the rcompiler(), ropenblas(), last_version_r(), last_version_openblas(), link_again() and rnews(). All of them are very simple to use and have few arguments that are sufficient to maintain the flexibility of use. Also, functions like rcompiler() and ropenblas() do not return content or data structures that are of any practical use. What these functions do is configure the GNU/Linux system to use R, configure different versions of the language, switch between versions, and link with the OpenBLAS library. It is also possible to obtain a summary of the versions of R and the OpenBLAS library that are available.

Table 1 below presents the benefit of considering an optimized version of BLAS. Computational costs are presented in the calculation of the singular decomposition in a rectangular matrix (svd() function) and in the calculation of the inverse of that same matrix (solve() function). Some repetitions (100 repetitions) of each of the respective functions were performed. The benchmark can be better observed through the violin plots shown in Figure 2.

| Functions | Library | Time (seconds) | |------------|----------|:--------------:| | svd(x) | BLAS | 6.520 | | svd(x) | OpenBLAS | 0.641 | | solve(x) | BLAS | 1.640 | | solve(x) | OpenBLAS | 0.640 |

: Comparison of the computational costs of the svd() and solve() functions (average of 100 repetitions).

Through a benchmark it is possible to better understand the performance gain that can be achieved by linking the R language to the OpenBLAS library. Figure 2 presents the benchmarks in the form of a violin plot, in which 100 reproductions of the svd(X) expression were considered, in the form of the code above, with the R linked to the BLAS library and linked to the OpenBLAS library, respectively, on the same hardware. It was observed that the average time of execution of the routine svd(X) considering the OpenBLAS library was less than 10 times the time necessary to execute it in R linking to a non-optimized version of BLAS, being the average time of 0.64 and 6.52 seconds, respectively.

\begin{figure}[H]

{\centering \includegraphics[width=0.5\linewidth]{benchmark}

}

\caption{Benchmarks of a decomposition of singular and inverse value of a matrix of dimension 1000 x 1000.}\label{fig:bench} \end{figure}

Improvements

The package will continue to evolve and code reviews will always be carried out. In addition, contributions to the development of the package are always welcome, especially those that aim to allow the rcompiler() and ropenblas() functions to work on Windows systems. There is also an interest that the ropenblas package will allow the linking of the Intel Math Kernel Library - MKL, just as it is done with the OpenBLAS library. All of these are improvements that we would like to see in future versions of the package.

References

prdm0/ropenblas documentation built on Sept. 6, 2022, 12:17 a.m.