BwUniCluster2.0/Software/R/terra
Note that the instructions provided below refer to R 4.4.1 (but not R 4.2.1)! UNDER CONSTRUCTION!!!
General information
terra is a R package for spatial data analysis with vectors (points, lines, polygons) and raster (grid) data.
sf is a R package that provides simple feature access for R.
In order to install those, we need to fulfill the following system requirements:
These packages are not available centrally on the cluster, but can be installed manually (to the $HOME-directory). Specifically, to install these packages, they need to be built from source.
Installation
Please enter the following code, presented in the boxes below, directly into your shell/command line on bwUniCluster.
The whole process will take approximately 45 minutes.
Preparations
Prepare .R directory (if it does not already exists). This is then filled with information how R should compile the packages (so-called 'compilation flags'). These are written (and can be reviewed) into the (text) file Makevars.
If you already have a .R/Makevars file, check whether these flags are already set.
cat ~/.R/Makevars
In this case, skip the following block of five commands. If not, please enter the following commands in your shell (command line):
mkdir -p ~/.R
echo "CXX14=icpc" > ~/.R/Makevars
echo "CXX17=icpc" >> ~/.R/Makevars
echo "CXX14FLAGS=-O3 -fPIC -std=c++14 -wd308 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" >> ~/.R/Makevars
echo "CXX17FLAGS=-O3 -fPIC -std=c++17 -wd308 -axCORE-AVX512,CORE-AVX2,AVX -xSSE4.2 -fp-model strict -qopenmp" >> ~/.R/Makevars
echo "CXXFLAGS += -wd308" >> ~/.R/Makevars
echo "PKG_CXXFLAGS += -std=c++14 -wd308" >> ~/.R/Makevars
Install external programs
First, we download the sources of GDAL, PROJ, GEOS and install the three programs.
We will gather them in a folder src, unpack there and then compile.
We strongly recommend to use a interactive session with multiple cores.
salloc -n 4 -t 60 -p single
First, provide the source directory (if not yet existing)
mkdir -p ~/src
cd ~/src
Then, download and install PROJ
PROJ_VER=9.3.1
wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz
tar xf proj-$PROJ_VER.tar.gz
cd proj-$PROJ_VER
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
cmake --build . -j 8
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-$GDAL_VER
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
cmake --build . -j 8
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 -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=$HOME/sw/R ..
make -j 8
ctest -j 8
make install
Installing the R packages
In order to install the two R packages, we need R to understand where we installed the 3 underlying programs, so we export the necessary paths.
export LD_LIBRARY_PATH=$HOME/sw/R/lib64:$LD_LIBRARY_PATH
export PATH=$PATH:$HOME/sw/R/bin
export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib64/pkgconfig
export GDAL_DATA=$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$HOME/sw/R/include
export CXX="icpc -std=c++11"
export CXX17=icpc
Now, we install terra and sf from within R.
module load math/R/4.1.2
R -q
R> install.packages("terra")
R> library(terra)
terra 1.7.71
R> install.packages("sf")
R> library(sf)
Linking to GEOS 3.12.1, GDAL 3.8.3, PROJ 9.3.1; sf_use_s2() is TRUE
Preparations to use the terra and sf packages
Since terra and sf depend on the external programs we installed, several environment variables have to be set before using the packages to allow R to address these programs.
We recommend to add the export commands
export LD_LIBRARY_PATH=$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
to your batch job scripts that use terra and sf or to run them directly in the command line if you use an interactive session.