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

K Kuck at 16:08, 30 October 2024

2024-10-30T16:08:44Z

← Older revision		Revision as of 18:08, 30 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 4.4.1)! We are currently updating our guides for R 4.4.1.</b></span>

	= General information =		= General information =

	rstan provides the R interface for [https://mc-stan.org/ Stan], a platform for statistical modeling and high-performance statistical computation.		<code>rstan</code> provides the R interface for [https://mc-stan.org/ Stan], a platform for statistical modeling and high-performance statistical computation.

	To be compatible with our R installation, we recommend to install the development version of rstan.		To be compatible with our R installation, we recommend to install the development version of rstan.

	= Installation =		= Installation instructions =

	Please enter the following code, presented in the boxes below, directly in your shell/command line on '''bwUniCluster2.0'''.		Please enter the following code, presented in the boxes below, directly in your shell/command line on '''bwUniCluster2.0'''.

	== Preparations ==		== Preparations ==
			Installing <code>glmnet</code> involves compiling source code. Therefore, ensure that the following flags are set in <code>$HOME/.R/Makevars</code>:
	Prepare .R directory (if it does not already exists). This is then filled with information how R should compile the packages ('compilation flags'). These are written (and can be reviewed) into the (text) file Makevars.

	If you already have a .R/Makevars file, check whether these flags are already set.

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

			CXX14=g++
	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).
			CXX17=g++
			CXX14FLAGS += -std=c++14
			CXX17FLAGS += -std=c++17
			CXXFLAGS = -O3 -fPIC -march=cascadelake -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option
		⚫	</pre>

			If necessary, the appropriate compiler flags can be set by running the following lines of code:
	<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 -march=cascadelake -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>

			Since installing <code>glmnet</code> involves compiling, we start an <b>interactive session</b> on one of the compute nodes:
	The installation of rstan and its dependencies makes use other libraries (TBB, Threading Building Blocks) which need to be loaded before installation (and R, of course).

	<pre>		<pre>
		⚫	salloc -n 1 -t 30 -p dev_single
	module purge
⚫	module load math/R/4.1.2
	module load devel/tbb/2021.4.0
	</pre>		</pre>


	The installation process of rstan and its dependencies (Rcpp) needs input of how to use the TBB module. This is provided via specific environment variables. We also need to provide a further configuration information to install the R package v8 rstan depends on.
			Within the interactive session, load the R 4.4.1 module and provide configuration information to install the R package <code>v8</code>, rstan depends on.

	<pre>		<pre>
			# Load the R software module:
	export TBB_LIB=$TBB_LIB_DIR
		⚫	module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3
	export TBB_INC=$TBB_INC_DIR

	export TBB_INTERFACE_NEW='true'
			# Provide configuration information for the v8 R package
	export DOWNLOAD_STATIC_LIBV8=1		export DOWNLOAD_STATIC_LIBV8=1
	</pre>		</pre>

	== Installing the R package(s) [takes roughly 20 min] ==		== Installing the R package(s) [takes roughly 20 min] ==
			Now, start <code>R</code> and install <code>RStan</code> using the lines of code below:
	We can now install rstan (in its development version) and its dependencies within a R session

	Consider starting an interactive job for compiling. You need at most 5000MB total memory, e.g. start

	<pre>
⚫	salloc ~~-t 30~~ -n 1 -~~-mem=5000~~ -p dev_single
	</pre>

	Now, start R and install

	<pre>		<pre>
Line 69:		Line 60:
	</pre>		</pre>

	== Testing the installation ==		== Testing the installation ==

	To check whether the installation worked, make a test run in R		To check whether the installation worked, make a test run in R
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	> example(stan_model, package = "rstan", run.dontrun = TRUE)		> example(stan_model, package = "rstan", run.dontrun = TRUE)
	</pre>		</pre>

	= Preparations to use the rstan package =
	To run its applications, rstan compiles new scripts. For this, it again uses TBB, so you need to set the corresponding environment variables whenever you use rstan - as well as to load the R and TBB modules.


	For this, we recommend to add the modules

	<pre>
	module load math/R/4.1.2
	module load devel/tbb/2021.4.0
	</pre>


	as well as the three export commands

	<pre>
	export TBB_LIB=$TBB_LIB_DIR
	export TBB_INC=$TBB_INC_DIR
	export TBB_INTERFACE_NEW='true'
	</pre>

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

K Kuck at 13:23, 30 October 2024

2024-10-30T13:23:01Z

← Older revision		Revision as of 15:23, 30 October 2024
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	<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 4.2.1 (but not R 4.4.1)! We are currently updating our guides for R 4.4.1.</b></span>

	= General information =		= General information =

K Kuck at 07:53, 18 June 2024

2024-06-18T07:53:30Z

← Older revision		Revision as of 09:53, 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.</span>		<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 at 07:51, 18 June 2024

2024-06-18T07:51:11Z

← Older revision		Revision as of 09:51, 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.</span>

	= General information =		= General information =

H Winkhardt: /* Installation */

2024-05-02T09:00:10Z

Installation

← Older revision		Revision as of 11:00, 2 May 2024
Line 7:		Line 7:
	= Installation =		= Installation =

	Please enter the following code, presented in the boxes below, directly in your shell/command line on ~~bwUniCluster~~		Please enter the following code, presented in the boxes below, directly in your shell/command line on '''bwUniCluster2.0'''.

	== Preparations ==		== Preparations ==

K Kuck: Updated to include definition of C++17

2023-12-11T13:25:48Z

Updated to include definition of C++17

← Older revision		Revision as of 15:25, 11 December 2023
Line 23:		Line 23:
	mkdir -p ~/.R		mkdir -p ~/.R
	echo "CXX14=icpc" >> ~/.R/Makevars		echo "CXX14=icpc" >> ~/.R/Makevars
			echo "CXX17=icpc" >> ~/.R/Makevars
	echo "CXX14FLAGS=-O3 -fPIC -std=c++14 -wd308 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" >> ~/.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 +~~= -std=c++14 -wd308" >> ~/.R/Makevars		echo "CXX17FLAGS=-O3 -fPIC -std=c++17 -wd308 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" >> ~/.R/Makevars
			echo "CXXFLAGS += -wd308" >> ~/.R/Makevars
	echo "PKG_CXXFLAGS += -std=c++14 -wd308" >> ~/.R/Makevars		echo "PKG_CXXFLAGS += -std=c++14 -wd308" >> ~/.R/Makevars
	</pre>		</pre>

S Richling at 12:42, 14 March 2023

2023-03-14T12:42:06Z

← Older revision		Revision as of 14:42, 14 March 2023
Line 94:		Line 94:

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

	----
	[[Category:BwUniCluster]]
	[[Category:BwUniCluster_2.0]]

M Janczyk: M Janczyk moved page Rstan to BwUniCluster2.0/Software/R/Rstan

2023-03-14T09:53:24Z

M Janczyk moved page Rstan to BwUniCluster2.0/Software/R/Rstan

← Older revision	Revision as of 11:53, 14 March 2023
(No difference)

F Freund: /* Installation */

2022-07-06T06:54:20Z

Installation

← Older revision		Revision as of 08:54, 6 July 2022
Line 7:		Line 7:
	= Installation =		= Installation =

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

	== Preparations ==		== Preparations ==
Line 18:		Line 18:
	</pre>		</pre>

	In this case, skip the following ~~five~~ ~~command~~ ~~block~~. If this is not the case, enter the following commands on 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).

	<pre>		<pre>
Line 48:		Line 48:
	We can now install rstan (in its development version) and its dependencies within a R session		We can now install rstan (in its development version) and its dependencies within a R session

	Consider starting an interactive job for compiling. You need at ~~least~~ 5000MB total memory, e.g. start		Consider starting an interactive job for compiling. You need at most 5000MB total memory, e.g. start

	<pre>		<pre>

F Freund: /* Preparations */

2022-07-06T06:52:41Z

Preparations

← Older revision		Revision as of 08:52, 6 July 2022
Line 18:		Line 18:
	</pre>		</pre>

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

	<pre>		<pre>