Difference between revisions of "BwUniCluster2.0/Software/R/Rjags"
< BwUniCluster2.0 | Software | R
(→Installation instructions: JAGS build using Intel Compiler & Intel MKL) |
m (M Janczyk moved page Rjags to BwUniCluster2.0/Software/R/Rjags) |
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| − | = Installation instructions: JAGS build using Intel Compiler & Intel MKL = |
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| + | = General information = |
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| − | Requirements: R, Intel compiler >= 17.0, Intel MKL >= 2017 |
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| + | 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 |
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| − | Consider starting an interactive job for compiling. Copy and paste the following to your shell. |
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| + | |||
| + | 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. |
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| + | |||
| + | |||
| + | = Installation = |
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| + | |||
| + | Please enter the following code, presented in the boxes below, directly into your shell/command line on bwUniCluster |
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<pre> |
<pre> |
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| − | # |
+ | #Load R module |
| − | module load math/R/ |
+ | module load math/R/4.1.2 |
| − | # Check compiler and MKL version (see, requirements) |
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| − | module list |
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| − | # Set up JAGS installation directory |
+ | # Set up JAGS installation directory |
export JAGS_HOME=$HOME/sw/jags |
export JAGS_HOME=$HOME/sw/jags |
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| + | |||
| − | # Prepare JAGS source directory |
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| + | # Prepare JAGS source directory (if not yet existing) |
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mkdir -p ~/src |
mkdir -p ~/src |
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cd ~/src |
cd ~/src |
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| − | # Get JAGS |
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| − | wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.0.tar.gz |
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| − | tar xf JAGS-4.3.0.tar.gz |
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| − | cd JAGS-4.3.0 |
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| − | # |
+ | # Get JAGS source |
| + | wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.1.tar.gz |
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| + | tar xf JAGS-4.3.1.tar.gz |
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| + | cd JAGS-4.3.1 |
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| + | rm JAGS-4.3.1.tar.gz |
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| + | |||
| + | |||
| + | # Install JAGS |
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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" |
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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" |
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./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm" |
./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm" |
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| − | make |
+ | make |
make install |
make install |
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cd |
cd |
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| + | |||
# Set up environment |
# Set up environment |
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export PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig |
export PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig |
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export LD_RUN_PATH=$JAGS_HOME/lib |
export LD_RUN_PATH=$JAGS_HOME/lib |
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| + | |||
# Install rjags package from within R session |
# Install rjags package from within R session |
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R -q |
R -q |
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| − | install.packages("rjags", configure.args="--enable-rpath") |
+ | > install.packages("rjags", configure.args="--enable-rpath") |
| + | > library(rjags) |
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| − | </pre> |
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| + | |||
| + | ---- |
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| + | [[Category:BwUniCluster]] |
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| + | [[Category:BwUniCluster_2.0]] |
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Latest revision as of 11:53, 14 March 2023
1 General information
rjags is a R interface to use JAGS, Just another Gibbs Sampler. JAGS is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
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.
2 Installation
Please enter the following code, presented in the boxes below, directly into your shell/command line on bwUniCluster
#Load R module module load math/R/4.1.2 # Set up JAGS installation directory export JAGS_HOME=$HOME/sw/jags # Prepare JAGS source directory (if not yet existing) mkdir -p ~/src cd ~/src # Get JAGS source wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.1.tar.gz tar xf JAGS-4.3.1.tar.gz cd JAGS-4.3.1 rm JAGS-4.3.1.tar.gz # Install JAGS export CFLAGS="-O3 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" export CXXFLAGS="-O3 -std=c++14 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" ./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm" make make install cd # Set up environment export PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig export LD_RUN_PATH=$JAGS_HOME/lib # Install rjags package from within R session R -q > install.packages("rjags", configure.args="--enable-rpath") > library(rjags)
