Difference between revisions of "BwUniCluster2.0/Software/R/Rjags"
< BwUniCluster2.0 | Software | R
(Created page with "= Installation instructions = Consider starting an interactive job for compiling. Just copy paste this to your shell (please only copy line by line so you see errors fast). ...") |
(→Installation instructions) |
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| − | = Installation instructions = |
+ | = Installation instructions: JAGS build using Intel Compiler & Intel MKL = |
| + | Requirements: R >= 3.4.4, Intel compiler >= 17.0, Intel MKL >= 2017 |
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| − | Consider starting an interactive job for compiling. Just copy paste this to your shell (please only copy line by line so you see errors fast). |
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| + | |||
| + | Consider starting an interactive job for compiling. Copy and paste the following to your shell. |
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<pre> |
<pre> |
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| − | module load math/R |
+ | module load math/R/3.5.1 |
| + | |||
| + | # Check compiler and MKL version (see, requirements) |
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| + | module list |
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| + | |||
| + | # Set up JAGS installation directory |
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| + | export JAGS_HOME=$HOME/sw/jags |
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| + | |||
| + | # Prepare JAGS source directory |
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mkdir -p ~/src |
mkdir -p ~/src |
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cd ~/src |
cd ~/src |
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| − | # copy the JAGS-4.3.0.tar.gz here |
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| − | # |
+ | # Get JAGS |
| + | wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.0.tar.gz |
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tar xf JAGS-4.3.0.tar.gz |
tar xf JAGS-4.3.0.tar.gz |
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cd JAGS-4.3.0 |
cd JAGS-4.3.0 |
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| + | |||
| − | ./configure --prefix=$HOME/sw |
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| + | # Build JAGS |
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| − | make -j4 |
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| + | export CFLAGS="-O3 -fPIC -fp-model strict -qopenmp -xHost" |
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| + | export CXXFLAGS="-O3 -fPIC -std=c++11 -fp-model strict -qopenmp -xHost" |
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| + | ./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm" |
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| + | make -j8 |
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make install |
make install |
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| − | cd |
+ | cd |
| − | # Set up environment |
+ | # Set up environment |
| − | export |
+ | export PKG_CONFIG_PATH=$JAGS_HOME/lib/pkgconfig |
| − | export |
+ | export LD_RUN_PATH=$JAGS_HOME/lib |
| − | export MANPATH=$MANPATH:$HOME/sw/man |
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| − | export CFLAGS=-I$HOME/sw/include |
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| − | export JAGS_LIBDIR=~/sw/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") |
+ | install.packages("rjags", configure.args="--enable-rpath") |
| − | library("rjags") |
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</pre> |
</pre> |
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Revision as of 20:36, 18 October 2018
Installation instructions: JAGS build using Intel Compiler & Intel MKL
Requirements: R >= 3.4.4, Intel compiler >= 17.0, Intel MKL >= 2017
Consider starting an interactive job for compiling. Copy and paste the following to your shell.
module load math/R/3.5.1
# Check compiler and MKL version (see, requirements)
module list
# Set up JAGS installation directory
export JAGS_HOME=$HOME/sw/jags
# Prepare JAGS source directory
mkdir -p ~/src
cd ~/src
# Get JAGS
wget https://sourceforge.net/projects/mcmc-jags/files/JAGS/4.x/Source/JAGS-4.3.0.tar.gz
tar xf JAGS-4.3.0.tar.gz
cd JAGS-4.3.0
# Build JAGS
export CFLAGS="-O3 -fPIC -fp-model strict -qopenmp -xHost"
export CXXFLAGS="-O3 -fPIC -std=c++11 -fp-model strict -qopenmp -xHost"
./configure --prefix=$JAGS_HOME --with-blas="-lmkl_rt -lpthread -lm"
make -j8
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")
