2024-10-28T17:28:33Z

K Kuck: /* Install glmnet */

Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)!

= General information =
<code>glmnet</code> is an <code>R</code> package that fits generalized linear and similar models via penalized maximum likelihood, particularly, lasso and elastic-net.

= Installation instructions =
== Preparations ==
Installing <code>glmnet</code> involves compiling source code. Therefore, ensure that the following flags are set in <code>$HOME/.R/Makevars</code>:

<pre>
cat ~/.R/Makevars

CXX14=g++
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>
mkdir -p ~/.R
echo "CXX14=g++" > ~/.R/Makevars
echo "CXX17=g++" >> ~/.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 "CXX14FLAGS += -std=c++14" >> ~/.R/Makevars
echo "CXX17FLAGS += -std=c++17" >> ~/.R/Makevars
</pre>

Since installing <code>glmnet</code> involves compiling, we start an interactive session on one of the compute nodes:
<pre>
salloc -n 1 -t 30 -p dev_single
</pre>

== Install <code>glmnet</code> ==
<pre>
# Load the R software module:
module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3

# Install the glmnet package from within R session
R -q

R> install.packages("RcppEigen", configure.vars = "CXXFLAGS='-O3 -fPIC -march=cascadelake -ffp-contract=off -fno-fast-math -fno-signed-zeros -fopenmp -Wno-unknown-warning-option'")

R> install.packages("glmnet")
</pre>

== Test the installation ==
As a quick test of the installation of <code>glmnet</code> the following lines of code can be run:

<pre>
# Run a quick test
> library(glmnet)
> data(QuickStartExample)
> x <- QuickStartExample$x
> y <- QuickStartExample$y
> fit <- glmnet(x, y)
> print(fit)
</pre>

BwUniCluster2.0/Software/R/Glmnet

2024-10-28T16:48:59Z

K Kuck:

K Kuck: /* Preparations */

Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)! UNDER CONSTRUCTION!!!

= General information =
[https://rspatial.github.io/terra/ '''terra'''] is a R package for spatial data analysis with vectors (points, lines, polygons) and raster (grid) data.

[https://github.com/r-spatial/sf '''sf'''] is a R package that provides [https://en.wikipedia.org/wiki/Simple_Features simple feature] access for R.

In order to install those, we need to fulfill the following [https://cran.r-project.org/web/packages/terra/index.html system requirements]:
* [https://gdal.org/ GDAL] 2.2.3 or higher
* [https://proj.org/ PROJ] 4.9.3 or higher
* [https://libgeos.org/ GEOS] 3.4.0 or higher

These packages are not available centrally on the cluster, but can be installed manually (to the <code>$HOME</code>-directory). Specifically, to install these packages, they need to be built from source.

= Installation =

Please enter (or copy & paste) the code, presented in the boxes below, directly into your shell/command line on bwUniCluster. The whole process will take approximately 45 minutes.

First, for compilation we obtain an interactive session (on a compute node):
<pre>
# Obtain interactive session
salloc -n 8 -t 60 -p single
</pre>

== Preparations ==
Prepare an <code>.R/Makevars</code> file (if it does not already exists). 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:
<pre>
# Ensure that the ~/.R/Makevars file has the following lines:
cat $HOME/.R/Makevars

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

Please run the following lines of code to set the flags, if necessary:
<pre>
mkdir -p ~/.R
echo "CXX14=g++" > ~/.R/Makevars
echo "CXX17=g++" >> ~/.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 "CXX14FLAGS += -std=c++14" >> ~/.R/Makevars
echo "CXX17FLAGS += -std=c++17" >> ~/.R/Makevars
</pre>

Next, we create the directories for the source code and installation targets, respectively. Furthermore, we load all (software) modules relevant for compilation and ensure that the compilers are found:

<pre>
# We install the libraries into the ~/sw/R directory.
mkdir -p ~/sw/R

# Source directory.
mkdir -p ~/src

# Load required modules.
module purge
module load devel/cmake/3.29.3
module load devel/python/3.12.3_gnu_13.3

# Check that the GNU compiler 13.3 is loaded.
gcc --version

# Set compiler for cmake and make.
export CC=$(which gcc)
export CXX=$(which g++)
</pre>

The Python 3.12.3 module is missing some required packages which are included in the Python default module. Therefore, we install them in the user environment:
<pre>
pip3 install --user numpy setuptools
</pre>

== Install external programs ==

First, we download the sources of GDAL, PROJ, GEOS (and their dependencies) and install them:

=== Install PROJ ===
<pre>
# Download and unpack the PROJ source code:
PROJ_VER=9.4.1
cd $HOME/src
wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz
tar xf proj-$PROJ_VER.tar.gz

cd proj-$PROJ_VER
mkdir build && cd build

# Compile and install PROJ:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" ..
cmake --build . -j 8
cmake --build . --target install
</pre>

=== Install GDAL ===
Building GDAL requires newer versions of <code>OpenEXR</code> and <code>libdeflate</code> then available on the system.

<pre>
# Download and unpack the libdeflate source code:
cd $HOME/src
git clone https://github.com/ebiggers/libdeflate

cd libdeflate
mkdir build && cd build

# Compile libdeflate
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install

# Download and unpack the OpenEXR source code:
OPENEXR_VER=3.3.1
cd $HOME/src
wget https://github.com/AcademySoftwareFoundation/openexr/releases/download/v$OPENEXR_VER/openexr-$OPENEXR_VER.tar.gz
tar xf openexr-$OPENEXR_VER.tar.gz

cd openexr-$OPENEXR_VER/
mkdir build && cd build

# Compile OpenEXR:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" -DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install
</pre>

Now, all necessary dependencies are available and we can build <code>GDAL</code>:

<pre>
# Download and unpack the GDAL source code:
cd $HOME/src
GDAL_VER=3.9.3
wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz
tar xf gdal-$GDAL_VER.tar.gz

cd gdal-$GDAL_VER
mkdir build && cd build

cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install
</pre>

=== Install GEOS ===

The last package that needs to be compiled is GEOS:
<pre>
# Download and unpack the GEOS source code.
cd $HOME/src
GEOS_VER=3.13.0
wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2
tar xf geos-$GEOS_VER.tar.bz2

cd geos-$GEOS_VER
mkdir build && cd build

# Compile GEOS:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
make -j 8
ctest -j 8
make install
</pre>

== Installing the R packages ==

In order to install the two R packages, we need to inform R where to find <code>PROJ</code>, <code>GDAL</code> and <code>GEOS</code>, so we export the necessary paths:

<pre>

export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal
</pre>

Additionally, the R package installation features compilation of built-in C++ code, for which we specify compilation options ('compiler flags')

<pre>
export CFLAGS=-I$HOME/sw/R/include
</pre>

Now, we install <code>terra</code> and <code>sf</code> from within <code>R</code>.

<pre>
module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3

R -q
R> install.packages("terra")
R> library(terra)
terra 1.7.83

R> install.packages("sf")
R> library(sf)
Linking to GEOS 3.13.0, GDAL 3.9.3, PROJ 9.4.1; sf_use_s2() is TRUE

</pre>

== Preparations to use the terra and sf packages ==
Since terra and sf depend on the external programs we installed, several environment variables have to be set before using the packages to allow R to address these programs.

We recommend to add the export commands

<pre>
export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal
</pre>

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

BwUniCluster2.0/Software/R/terra

2024-10-28T15:33:02Z

K Kuck: /* Installing the R packages */

Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)! UNDER CONSTRUCTION!!!

= General information =
[https://rspatial.github.io/terra/ '''terra'''] is a R package for spatial data analysis with vectors (points, lines, polygons) and raster (grid) data.

[https://github.com/r-spatial/sf '''sf'''] is a R package that provides [https://en.wikipedia.org/wiki/Simple_Features simple feature] access for R.

In order to install those, we need to fulfill the following [https://cran.r-project.org/web/packages/terra/index.html system requirements]:
* [https://gdal.org/ GDAL] 2.2.3 or higher
* [https://proj.org/ PROJ] 4.9.3 or higher
* [https://libgeos.org/ GEOS] 3.4.0 or higher

These packages are not available centrally on the cluster, but can be installed manually (to the <code>$HOME</code>-directory). Specifically, to install these packages, they need to be built from source.

= Installation =

Please enter (or copy & paste) the code, presented in the boxes below, directly into your shell/command line on bwUniCluster. The whole process will take approximately 45 minutes.

First, for compilation we obtain an interactive session (on a compute node):
<pre>
# Obtain interactive session
salloc -n 8 -t 60 -p single
</pre>

== Preparations ==
Prepare an <code>.R/Makevars</code> file (if it does not already exists). 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:
<pre>
# Ensure that the ~/.R/Makevars file has the following lines:
cat $HOME/.R/Makevars

CXX14=g++
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>

Please run the following lines of code to set the flags, if necessary:
<pre>
mkdir -p ~/.R
echo "CXX14=g++" > ~/.R/Makevars
echo "CXX17=g++" >> ~/.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 "CXX14FLAGS += -std=c++14" >> ~/.R/Makevars
echo "CXX17FLAGS += -std=c++17" >> ~/.R/Makevars
</pre>

Next, we create the directories for the source code and installation targets, respectively. Furthermore, we load all (software) modules relevant for compilation and ensure that the compilers are found:

<pre>
# We install the libraries into the ~/sw/R directory.
mkdir -p ~/sw/R

# Source directory.
mkdir -p ~/src

# Load required modules.
module purge
module load devel/cmake/3.29.3
module load devel/python/3.12.3_gnu_13.3

# Check that the GNU compiler 13.3 is loaded.
gcc --version

# Set compiler for cmake and make.
export CC=$(which gcc)
export CXX=$(which g++)
</pre>

The Python 3.12.3 module is missing some required packages which are included in the Python default module. Therefore, we install them in the user environment:
<pre>
pip3 install --user numpy setuptools
</pre>

== Install external programs ==

First, we download the sources of GDAL, PROJ, GEOS (and their dependencies) and install them:

=== Install PROJ ===
<pre>
# Download and unpack the PROJ source code:
PROJ_VER=9.4.1
cd $HOME/src
wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz
tar xf proj-$PROJ_VER.tar.gz

cd proj-$PROJ_VER
mkdir build && cd build

# Compile and install PROJ:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" ..
cmake --build . -j 8
cmake --build . --target install
</pre>

=== Install GDAL ===
Building GDAL requires newer versions of <code>OpenEXR</code> and <code>libdeflate</code> then available on the system.

<pre>
# Download and unpack the libdeflate source code:
cd $HOME/src
git clone https://github.com/ebiggers/libdeflate

cd libdeflate
mkdir build && cd build

# Compile libdeflate
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install

# Download and unpack the OpenEXR source code:
OPENEXR_VER=3.3.1
cd $HOME/src
wget https://github.com/AcademySoftwareFoundation/openexr/releases/download/v$OPENEXR_VER/openexr-$OPENEXR_VER.tar.gz
tar xf openexr-$OPENEXR_VER.tar.gz

cd openexr-$OPENEXR_VER/
mkdir build && cd build

# Compile OpenEXR:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" -DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install
</pre>

Now, all necessary dependencies are available and we can build <code>GDAL</code>:

<pre>
# Download and unpack the GDAL source code:
cd $HOME/src
GDAL_VER=3.9.3
wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz
tar xf gdal-$GDAL_VER.tar.gz

cd gdal-$GDAL_VER
mkdir build && cd build

cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install
</pre>

=== Install GEOS ===

The last package that needs to be compiled is GEOS:
<pre>
# Download and unpack the GEOS source code.
cd $HOME/src
GEOS_VER=3.13.0
wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2
tar xf geos-$GEOS_VER.tar.bz2

cd geos-$GEOS_VER
mkdir build && cd build

# Compile GEOS:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
make -j 8
ctest -j 8
make install
</pre>

== Installing the R packages ==

In order to install the two R packages, we need to inform R where to find <code>PROJ</code>, <code>GDAL</code> and <code>GEOS</code>, so we export the necessary paths:

<pre>

export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal
</pre>

Additionally, the R package installation features compilation of built-in C++ code, for which we specify compilation options ('compiler flags')

<pre>
export CFLAGS=-I$HOME/sw/R/include
</pre>

Now, we install <code>terra</code> and <code>sf</code> from within <code>R</code>.

<pre>
module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3

R -q
R> install.packages("terra")
R> library(terra)
terra 1.7.83

R> install.packages("sf")
R> library(sf)
Linking to GEOS 3.13.0, GDAL 3.9.3, PROJ 9.4.1; sf_use_s2() is TRUE

</pre>

== Preparations to use the terra and sf packages ==
Since terra and sf depend on the external programs we installed, several environment variables have to be set before using the packages to allow R to address these programs.

We recommend to add the export commands

<pre>
export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal
</pre>

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

BwUniCluster2.0/Software/R/terra

2024-10-28T15:31:19Z

K Kuck: /* Installing the R packages */

Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)! UNDER CONSTRUCTION!!!

= General information =
[https://rspatial.github.io/terra/ '''terra'''] is a R package for spatial data analysis with vectors (points, lines, polygons) and raster (grid) data.

[https://github.com/r-spatial/sf '''sf'''] is a R package that provides [https://en.wikipedia.org/wiki/Simple_Features simple feature] access for R.

In order to install those, we need to fulfill the following [https://cran.r-project.org/web/packages/terra/index.html system requirements]:
* [https://gdal.org/ GDAL] 2.2.3 or higher
* [https://proj.org/ PROJ] 4.9.3 or higher
* [https://libgeos.org/ GEOS] 3.4.0 or higher

These packages are not available centrally on the cluster, but can be installed manually (to the <code>$HOME</code>-directory). Specifically, to install these packages, they need to be built from source.

= Installation =

Please enter (or copy & paste) the code, presented in the boxes below, directly into your shell/command line on bwUniCluster. The whole process will take approximately 45 minutes.

First, for compilation we obtain an interactive session (on a compute node):
<pre>
# Obtain interactive session
salloc -n 8 -t 60 -p single
</pre>

== Preparations ==
Prepare an <code>.R/Makevars</code> file (if it does not already exists). 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:
<pre>
# Ensure that the ~/.R/Makevars file has the following lines:
cat $HOME/.R/Makevars

CXX14=g++
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>

Please run the following lines of code to set the flags, if necessary:
<pre>
mkdir -p ~/.R
echo "CXX14=g++" > ~/.R/Makevars
echo "CXX17=g++" >> ~/.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 "CXX14FLAGS += -std=c++14" >> ~/.R/Makevars
echo "CXX17FLAGS += -std=c++17" >> ~/.R/Makevars
</pre>

Next, we create the directories for the source code and installation targets, respectively. Furthermore, we load all (software) modules relevant for compilation and ensure that the compilers are found:

<pre>
# We install the libraries into the ~/sw/R directory.
mkdir -p ~/sw/R

# Source directory.
mkdir -p ~/src

# Load required modules.
module purge
module load devel/cmake/3.29.3
module load devel/python/3.12.3_gnu_13.3

# Check that the GNU compiler 13.3 is loaded.
gcc --version

# Set compiler for cmake and make.
export CC=$(which gcc)
export CXX=$(which g++)
</pre>

The Python 3.12.3 module is missing some required packages which are included in the Python default module. Therefore, we install them in the user environment:
<pre>
pip3 install --user numpy setuptools
</pre>

== Install external programs ==

First, we download the sources of GDAL, PROJ, GEOS (and their dependencies) and install them:

=== Install PROJ ===
<pre>
# Download and unpack the PROJ source code:
PROJ_VER=9.4.1
cd $HOME/src
wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz
tar xf proj-$PROJ_VER.tar.gz

cd proj-$PROJ_VER
mkdir build && cd build

# Compile and install PROJ:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" ..
cmake --build . -j 8
cmake --build . --target install
</pre>

=== Install GDAL ===
Building GDAL requires newer versions of <code>OpenEXR</code> and <code>libdeflate</code> then available on the system.

<pre>
# Download and unpack the libdeflate source code:
cd $HOME/src
git clone https://github.com/ebiggers/libdeflate

cd libdeflate
mkdir build && cd build

# Compile libdeflate
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install

# Download and unpack the OpenEXR source code:
OPENEXR_VER=3.3.1
cd $HOME/src
wget https://github.com/AcademySoftwareFoundation/openexr/releases/download/v$OPENEXR_VER/openexr-$OPENEXR_VER.tar.gz
tar xf openexr-$OPENEXR_VER.tar.gz

cd openexr-$OPENEXR_VER/
mkdir build && cd build

# Compile OpenEXR:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" -DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install
</pre>

Now, all necessary dependencies are available and we can build <code>GDAL</code>:

<pre>
# Download and unpack the GDAL source code:
cd $HOME/src
GDAL_VER=3.9.3
wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz
tar xf gdal-$GDAL_VER.tar.gz

cd gdal-$GDAL_VER
mkdir build && cd build

cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
cmake --build . -j 8
cmake --build . --target install
</pre>

=== Install GEOS ===

The last package that needs to be compiled is GEOS:
<pre>
# Download and unpack the GEOS source code.
cd $HOME/src
GEOS_VER=3.13.0
wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2
tar xf geos-$GEOS_VER.tar.bz2

cd geos-$GEOS_VER
mkdir build && cd build

# Compile GEOS:
cmake -DCMAKE_INSTALL_PREFIX="$HOME/sw/R" \
-DCMAKE_PREFIX_PATH="$HOME/sw/R" \
-DCMAKE_BUILD_TYPE=Release ..
make -j 8
ctest -j 8
make install
</pre>

== Installing the R packages ==

In order to install the two R packages, we need to inform R where to find <code>PROJ</code>, <code>GDAL</code> and <code>GEOS</code>, so we export the necessary paths:

<pre>

export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal
</pre>

Additionally, the R package installation features compilation of built-in C++ code, for which we specify compilation options ('compiler flags')

<pre>
export CFLAGS=-I$HOME/sw/R/include
export CXX="{$(which g++)} -std=c++11"
export CXX17=$(which g++)
</pre>

Now, we install <code>terra</code> and <code>sf</code> from within <code>R</code>.

<pre>
module load math/R/4.4.1-mkl-2022.2.1-gnu-13.3

R -q
R> install.packages("terra")
R> library(terra)
terra 1.7.83

R> install.packages("sf")
R> library(sf)
Linking to GEOS 3.13.0, GDAL 3.9.3, PROJ 9.4.1; sf_use_s2() is TRUE

</pre>

== Preparations to use the terra and sf packages ==
Since terra and sf depend on the external programs we installed, several environment variables have to be set before using the packages to allow R to address these programs.

We recommend to add the export commands

<pre>
export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal
</pre>

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