K Kuck: Created page with " 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. = General information = sf and terra allow to use the following tools for handling spatial structures in R * the 'Geospatial' Data Abstraction Library [https://gdal.org/ GDAL] * Projection/transformation operations from the [https://proj.org/ PROJ] library * Interface to the open source Geometry Engin..."

2024-10-28T11:39:27Z

Created page with " 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. = General information = sf and terra allow to use the following tools for handling spatial structures in R * the 'Geospatial' Data Abstraction Library [https://gdal.org/ GDAL] * Projection/transformation operations from the [https://proj.org/ PROJ] library * Interface to the open source Geometry Engin..."

New page

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.

= General information =

sf and terra allow to use the following tools for handling spatial structures in R

* the 'Geospatial' Data Abstraction Library [https://gdal.org/ GDAL]
* Projection/transformation operations from the [https://proj.org/ PROJ] library
* Interface to the open source Geometry Engine [https://libgeos.org/ GEOS]

= Installation =

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

The whole process will take approximately 45 minutes.

== Preparations ==
Prepare .R directory (if it does not already exists). This is then filled with information how R should compile the packages (so-called '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>
cat ~/.R/Makevars
</pre>

In this case, skip the following block of five commands. If not, please enter the following commands in your shell (command line):
<pre>
mkdir -p ~/.R

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 "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
</pre>

== Install external programs ==

First, we download the sources of GDAL, PROJ, GEOS and install the three programs.

We will gather them in a folder src, unpack there and then compile.

We strongly recommend to use a interactive session with multiple cores.

<pre>
salloc -n 4 -t 60 -p single
</pre>

First, provide the source directory (if not yet existing)
<pre>
mkdir -p ~/src
cd ~/src
</pre>

Then, download and install PROJ
<pre>
PROJ_VER=9.3.1
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

cmake -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
cmake --build . -j 8
cmake --build . --target install
</pre>

Then, install GDAL

<pre>
cd $HOME/src
GDAL_VER=3.8.3
wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz
tar xf gdal-$GDAL_VER.tar.gz
cd gdal-$GDAL_VER

mkdir build
cd build

cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
cmake --build . -j 8
cmake --build . --target install

</pre>

Finally, install GEOS
<pre>
cd $HOME/src
GEOS_VER=3.12.1
wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2
tar xf geos-$GEOS_VER.tar.bz2
cd geos-$GEOS_VER

mkdir _build
cd _build

cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
make -j 8
ctest -j 8
make install
</pre>

== Installing the R packages ==

In order to install the two R packages, we need R to understand where we installed the 3 underlying programs, 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="icpc -std=c++11"
export CXX17=icpc
</pre>

Now, we install terra and sf from within R.

<pre>
module load math/R/4.1.2

R -q
R> install.packages("terra")
R> library(terra)
terra 1.7.71

R> install.packages("sf")
R> library(sf)
Linking to GEOS 3.12.1, GDAL 3.8.3, PROJ 9.3.1; 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 (R 4.2.1) - Revision history