BwUniCluster2.0/Software/R/stringi: Difference between revisions

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<span style="color:red"><b>Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)! We are currently updating our guides for R 4.3.3. </b></span>
<span style="color:red"><b>Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)!</b></span>


= General information =
= General information =
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Prepare an <code>.R/Makevars</code> file (if it does not already exist). This file specifies how R should compile the packages (i.e., sets some 'compiler flags').
Prepare an <code>.R/Makevars</code> file (if it does not already exist). This file specifies how R should compile the packages (i.e., sets some 'compiler flags').


If an <code>.R/Makevars</code> file is present in your home directory (<code>$HOME</code>), check whether the flags displayed below are already set and apply adjustments, if necessary:
If an <code>.R/Makevars</code> file is present in your home directory (<code>$HOME</code>), check whether the flags displayed below are set and apply adjustments, if necessary:
<pre>
<pre>
cat ~/.R/Makevars
cat ~/.R/Makevars
Line 23: Line 23:
</pre>
</pre>


Please run the following lines of code to set the appropriate flags, if necessary:


In this case, skip the following block of five commands. If this is not the case, enter the following commands in your shell (command line).

<pre>
<pre>
mkdir -p ~/.R
mkdir -p ~/.R
echo "CXX14=icpc" >> ~/.R/Makevars
echo "CXX14=g++" > ~/.R/Makevars
echo "CXX17=icpc" >> ~/.R/Makevars
echo "CXX17=g++" >> ~/.R/Makevars
echo "CXX14FLAGS=-O3 -fPIC -std=c++14 -wd308 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" >> ~/.R/Makevars
echo "CXXFLAGS = -O3 -fPIC -mavx -mavx2 -mavx512f -msse4.2 -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option" >> ~/.R/Makevars
echo "CXX17FLAGS=-O3 -fPIC -std=c++17 -wd308 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" >> ~/.R/Makevars
echo "CXX14FLAGS += -std=c++14" >> ~/.R/Makevars
echo "CXXFLAGS += -wd308" >> ~/.R/Makevars
echo "CXX17FLAGS += -std=c++17" >> ~/.R/Makevars
echo "PKG_CXXFLAGS += -std=c++14 -wd308" >> ~/.R/Makevars
</pre>
</pre>


⚫
== Install the R package ==
The installation of stringi makes use other libraries ([https://icu.unicode.org/ C/C++ and Java libraries for Unicode and globalization], icu4c Intel) which need to be loaded before installation (and R, of course).
We can now install <code>stringi</code> and its dependencies within a R session. To get the most out of <code>stringi</code>, you are strongly encouraged to rely on the custom ICU4C 74.1 implementation bundled with <code>stringi</code>:


<pre>
<pre>
module purge
module purge
module load math/R
module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3
module load lib/icu4c/74.1_intel2021.4.0
</pre>


⚫
R -q


⚫
R> install.packages("stringi", configure.args="--disable-pkg-config")
⚫
== Installing the R package ==
We can now install stringi (in its development version) and its dependencies within a R session

<pre>
⚫
R -q
⚫
> install.packages("stringi")
</pre>
</pre>

This ensures maximum portability across all platforms (Windows and macOS users fetch the pre-compiled binaries from CRAN built precisely this way).


== Testing the installation ==
== Testing the installation ==
Line 62: Line 55:
[1] 5 5 1
[1] 5 5 1
</pre>
</pre>


Note that you always need to load
<pre>
module load math/R/4.1.2
module load lib/icu4c/74.1_intel2021.4.0
</pre>

to your [[BwUniCluster_2.0_Slurm_common_Features#sbatch_Examples | batch job scripts]] that use stringi or to run them directly in the command line if you use an [[BwUniCluster_2.0_Batch_Queues | interactive session]].

Latest revision as of 18:17, 28 October 2024

Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)!

General information

stringi is an R package for fast, portable, correct, consistent, and convenient string/text processing in any locale or character encoding.

Installation

Please enter the code, presented in the boxes below, directly in your shell/command line on bwUniCluster:

Preparations

Prepare an .R/Makevars file (if it does not already exist). This file specifies how R should compile the packages (i.e., sets some 'compiler flags').

If an .R/Makevars file is present in your home directory ($HOME), check whether the flags displayed below are set and apply adjustments, if necessary: 

cat ~/.R/Makevars

CXX14=g++ 
CXX17=g++
CXXFLAGS = -O3 -fPIC -mavx -mavx2 -mavx512f -msse4.2 -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option
CXX14FLAGS += -std=c++14
CXX17FLAGS += -std=c++17

Please run the following lines of code to set the appropriate flags, if necessary: 

mkdir -p ~/.R
echo "CXX14=g++" > ~/.R/Makevars
echo "CXX17=g++" >> ~/.R/Makevars
echo "CXXFLAGS = -O3 -fPIC -mavx -mavx2 -mavx512f -msse4.2 -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option" >> ~/.R/Makevars
echo "CXX14FLAGS += -std=c++14" >> ~/.R/Makevars
echo "CXX17FLAGS += -std=c++17" >> ~/.R/Makevars

Install the R package

We can now install stringi and its dependencies within a R session. To get the most out of stringi, you are strongly encouraged to rely on the custom ICU4C 74.1 implementation bundled with stringi: 

module purge
module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3

R -q

R> install.packages("stringi", configure.args="--disable-pkg-config")

This ensures maximum portability across all platforms (Windows and macOS users fetch the pre-compiled binaries from CRAN built precisely this way).

Testing the installation

To check whether the installation worked, make a test run in R 

> library(stringi)
> stri_length(c("Hello", "world", "!"))
[1] 5 5 1
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