BwUniCluster2.0/Software/R/terra

General information

Please note that THIS SITE IS UNDER CONSTRUCTION!!!

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

• the 'Geospatial' Data Abstraction Library GDAL
• Projection/transformation operations from the PROJ library
• Interface to the open source Geometry Engine 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 30 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.

cat ~/.R/Makevars

In this case, skip the following block of five commands. If not, please enter the following commands in your shell (command line):

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

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.

salloc -n 4 -t 30 -p dev_single

First, provide the source directory (if not yet existing)

mkdir -p ~/src
cd ~/src

Then, download and install PROJ

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

export CMAKE_BUILD_PARALLEL_LEVEL=8
cmake -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
cmake --build .
cmake --build . --target install

Then, install GDAL

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_BUILD_PARALLEL_LEVEL=8
cmake -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
cmake --build .
cmake --build . --target install

Finally, install GEOS

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_BUILD_PARALLEL_LEVEL=4
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
make
ctest
make install

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.

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/lib/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal

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

export CFLAGS=-I$HOME/sw/R/include
export CXX="icpc -std=c++11"
export CXX17=icpc

Now, we install terra and sf from within R.

module load math/R/4.1.2


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


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

Preparations to use the terra and sf packages

Since rgdal and rgeos 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

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/lib/pkgconfig
export GDAL_DATA=$HOME/sw/R/share/gdal

to your batch job scripts that use rgdal and rgeos or to run them directly in the command line if you use an interactive session.