BwUniCluster2.0/Software/R/stringi - Revision history

K Kuck at 16:17, 28 October 2024

2024-10-28T16:17:51Z

← Older revision		Revision as of 18:17, 28 October 2024
Line 1:		Line 1:
	<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 =

K Kuck: /* Testing the installation */

2024-10-28T16:04:43Z

Testing the installation

← Older revision		Revision as of 18:04, 28 October 2024
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	[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]].

K Kuck: /* Install the R package */

2024-10-28T16:04:08Z

Install the R package

← Older revision		Revision as of 18:04, 28 October 2024
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	<pre>		<pre>
			module purge
			module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3

	R -q		R -q

K Kuck: /* Installing the R package */

2024-10-28T16:03:28Z

Installing the R package

← Older revision		Revision as of 18:03, 28 October 2024
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	</pre>		</pre>

	== ~~Installing~~ the R package ==		== Install the R package ==
	We can now install stringi ~~(in its development version)~~ and its dependencies within a R session		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>
	R -q		R -q

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

K Kuck: /* Preparations */

2024-10-28T16:00:48Z

Preparations

← Older revision		Revision as of 18:00, 28 October 2024
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	</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>

	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).

	<pre>
	module purge
	module load math/R
	module load lib/icu4c/74.1_intel2021.4.0
	</pre>		</pre>

K Kuck: /* Preparations */

2024-10-28T15:58:14Z

Preparations

← Older revision		Revision as of 17:58, 28 October 2024
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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 44:		Line 44:
	module load lib/icu4c/74.1_intel2021.4.0		module load lib/icu4c/74.1_intel2021.4.0
	</pre>		</pre>


	== Installing the R package ==		== Installing the R package ==

K Kuck at 15:57, 28 October 2024

2024-10-28T15:57:07Z

← Older revision		Revision as of 17:57, 28 October 2024
Line 1:		Line 1:
	<span style="color:red"><b>Note that the instructions provided below refer to R 4.2.1 (but not R 4.3.3)! 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)! We are currently updating our guides for R 4.3.3. </b></span>

	= General information =		= General information =
Line 10:		Line 10:

	== Preparations ==		== Preparations ==
	Prepare .R ~~directory~~ (if it does not already ~~exists~~). This is ~~then filled with information~~ how R should compile the packages ('compiler flags'). ~~These are written (and can be reviewed) into the (text) file Makevars.~~		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 you already have a .R/Makevars file, check whether these flags are already set.

			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:
	<pre>		<pre>
	cat ~/.R/Makevars		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
	</pre>		</pre>



	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).		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).

K Kuck at 15:52, 28 October 2024

2024-10-28T15:52:46Z

← Older revision		Revision as of 17:52, 28 October 2024
Line 3:		Line 3:
	= General information =		= General information =

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

	= Installation =		= Installation =

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

	== Preparations ==		== Preparations ==

K Kuck at 07:52, 18 June 2024

2024-06-18T07:52:30Z

← Older revision		Revision as of 09:52, 18 June 2024
Line 1:		Line 1:
			<span style="color:red"><b>Note that the instructions provided below refer to R 4.2.1 (but not R 4.3.3)! We are currently updating our guides for R 4.3.3.</b></span>

	= General information =		= General information =

K Kuck: /* Testing the installation */

2024-01-17T13:11:38Z

Testing the installation

← Older revision		Revision as of 15:11, 17 January 2024
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	<pre>		<pre>
	> library(stringi)		> library(stringi)
	> stri_length(c("Hello", "world", "!")		> stri_length(c("Hello", "world", "!"))
	[1] 5 5 1		[1] 5 5 1
	</pre>		</pre>