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

K Kuck at 16:13, 30 October 2024

2024-10-30T16:13:33Z

← Older revision		Revision as of 18:13, 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 =

H Winkhardt: Formatierung

2024-08-30T13:49:12Z

Formatierung

← Older revision		Revision as of 15:49, 30 August 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.</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 07:50, 18 June 2024

2024-06-18T07:50:44Z

← Older revision		Revision as of 09:50, 18 June 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.</span>

	= General information =		= General information =

M Janczyk at 08:18, 21 May 2024

2024-05-21T08:18:49Z

← Older revision		Revision as of 10:18, 21 May 2024
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	> install.packages("rjags", configure.args="--enable-rpath")		> install.packages("rjags", configure.args="--enable-rpath")
	> library(rjags)		> library(rjags)

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

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

2023-03-14T09:53:18Z

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

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

F Freund: /* Installation */

2022-06-23T13:53:18Z

Installation

← Older revision		Revision as of 15:53, 23 June 2022
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	= Installation =		= Installation =

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

	<pre>		<pre>

F Freund at 10:06, 23 June 2022

2022-06-23T10:06:02Z

← Older revision		Revision as of 12:06, 23 June 2022
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	#Load R module		#Load R module
	module load math/R/4.1.2		module load math/R/4.1.2


	# Set up JAGS installation directory		# Set up JAGS installation directory
		⚫	export JAGS_HOME=$HOME/sw/jags


⚫	export JAGS_HOME=$HOME/sw/jags

	# Prepare JAGS source directory (if not yet existing)		# Prepare JAGS source directory (if not yet existing)

	mkdir -p ~/src		mkdir -p ~/src
	cd ~/src		cd ~/src
Line 25:		Line 24:

	# Get JAGS source		# Get JAGS source

	wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.1.tar.gz		wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.1.tar.gz
	tar xf JAGS-4.3.1.tar.gz		tar xf JAGS-4.3.1.tar.gz
	cd JAGS-4.3.1		cd JAGS-4.3.1
	rm JAGS-4.3.1.tar.gz		rm JAGS-4.3.1.tar.gz




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	export PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig		export PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig
	export LD_RUN_PATH=$JAGS_HOME/lib		export LD_RUN_PATH=$JAGS_HOME/lib



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	> install.packages("rjags", configure.args="--enable-rpath")		> install.packages("rjags", configure.args="--enable-rpath")
	> library(rjags)		> library(rjags)



	----		----

F Freund at 10:04, 23 June 2022

2022-06-23T10:04:55Z

← Older revision		Revision as of 12:04, 23 June 2022
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	= Installation instructions: JAGS build using Intel Compiler & Intel MKL =

			= General information =
	Requirements: R, Intel compiler >= 17.0, Intel MKL >= 2017

			rjags is a R interface to use JAGS, [https://mcmc-jags.sourceforge.io/ Just another Gibbs Sampler]. JAGS is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
	Consider starting an interactive job for compiling. Copy and paste the following to your shell.

			rjags needs a JAGS installation on the side. We recommend to compile via Intel compiler and with the Intel MKL library (Intel Math Kernel Library), which allows JAGS to use various efficient implementations of mathematical computations. These are, as of now, loaded alongside with the module R 4.1.2.


			= Installation =

	<pre>		<pre>
	# Load ~~the~~ R ~~software~~ module~~, e.g.~~		#Load R module
	module load math/R/3.6.3		module load math/R/4.1.2

		⚫	# Set up JAGS installation directory

	# Check compiler and MKL version (see, requirements)
	module list

⚫	# Set up JAGS installation directory
	export JAGS_HOME=$HOME/sw/jags		export JAGS_HOME=$HOME/sw/jags

	# Prepare JAGS source directory		# Prepare JAGS source directory (if not yet existing)

	mkdir -p ~/src		mkdir -p ~/src
	cd ~/src		cd ~/src

⚫	# ~~Get~~ JAGS
⚫	wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.0.tar.gz
⚫	tar xf JAGS-4.3.0.tar.gz
⚫	cd JAGS-4.3.0

	# ~~Build~~ JAGS		# Get JAGS source

		⚫	wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.1.tar.gz
		⚫	tar xf JAGS-4.3.1.tar.gz
		⚫	cd JAGS-4.3.1
			rm JAGS-4.3.1.tar.gz




		⚫	# Install JAGS
	export CFLAGS="-O3 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp"		export CFLAGS="-O3 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp"
	export CXXFLAGS="-O3 -std=c++14 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp"		export CXXFLAGS="-O3 -std=c++14 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp"
	./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm"		./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm"
	make ~~-j8~~		make
	make install		make install
	cd		cd


	# Set up environment		# Set up environment
	export PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig		export PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig
	export LD_RUN_PATH=$JAGS_HOME/lib		export LD_RUN_PATH=$JAGS_HOME/lib



	# Install rjags package from within R session		# Install rjags package from within R session
	R -q		R -q
	install.packages("rjags", configure.args="--enable-rpath")		> install.packages("rjags", configure.args="--enable-rpath")
			> library(rjags)
	</pre>



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

J Salk: /* Installation instructions: JAGS build using Intel Compiler & Intel MKL */

2021-03-31T11:14:18Z

Installation instructions: JAGS build using Intel Compiler & Intel MKL

← Older revision		Revision as of 13:14, 31 March 2021
Line 6:		Line 6:

	<pre>		<pre>
			# Load the R software module, e.g.
	module load math/R/3.5.1		module load math/R/3.6.3

	# Check compiler and MKL version (see, requirements)		# Check compiler and MKL version (see, requirements)
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	# Build JAGS		# Build JAGS
	export CFLAGS="-O3 -~~fPIC~~ -fp-model strict -qopenmp ~~-xHost~~"		export CFLAGS="-O3 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp"
	export CXXFLAGS="-O3 ~~-fPIC~~ -std=c++11 -fp-model strict -qopenmp ~~-xHost~~"		export CXXFLAGS="-O3 -std=c++14 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp"
	./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm"		./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm"
	make -j8		make -j8

F Wagner: /* Installation instructions: JAGS build using Intel Compiler & Intel MKL */

2018-10-19T09:48:49Z

Installation instructions: JAGS build using Intel Compiler & Intel MKL

← Older revision		Revision as of 11:48, 19 October 2018
Line 1:		Line 1:
	= Installation instructions: JAGS build using Intel Compiler & Intel MKL =		= Installation instructions: JAGS build using Intel Compiler & Intel MKL =

	Requirements: R ~~>= 3.4.4~~, Intel compiler >= 17.0, Intel MKL >= 2017		Requirements: R, Intel compiler >= 17.0, Intel MKL >= 2017

	Consider starting an interactive job for compiling. Copy and paste the following to your shell.		Consider starting an interactive job for compiling. Copy and paste the following to your shell.