Difference between revisions of "BwUniCluster2.0/Software/R/Rgdal"
< BwUniCluster2.0 | Software | R
(Installation of rgdal/rgeos) |
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| − | = Installation instructions = |
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| + | = General information = |
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| − | Consider starting an interactive job for compiling. Copy and paste the following to your shell. |
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| + | Installation of rgdal and rgeos allows to use the following tools for handling spatial structures in R |
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| + | |||
| + | * the 'Geospatial' Data Abstraction Library [https://gdal.org/ GDAL] |
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| + | * Projection/transformation operations from the [https://proj.org/ PROJ] library |
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| + | * Interface to the open source Geometry Engine [https://libgeos.org/ GEOS] |
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| + | |||
| + | = Installation = |
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| + | |||
| + | Please enter the following code, presented in the boxes below, directly into your shell/command line on bwUniCluster. |
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| + | |||
| + | == Install external programs == |
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| + | |||
| + | First, we download the sources of GDAL, PROJ, GEOS and install the three programs. |
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| + | |||
| + | We will gather them in a folder src, unpack there and then compile. |
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| + | |||
| + | We strongly recommend to use a interactive session with multiple cores. |
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| + | |||
| + | <pre> |
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| + | salloc -n 4 -t 30 -p dev_single |
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| + | </pre> |
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| + | |||
| + | |||
| + | First, provide the source directory (if not yet existing) |
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<pre> |
<pre> |
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| − | module load math/R |
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| − | # Get sources |
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mkdir -p ~/src |
mkdir -p ~/src |
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cd ~/src |
cd ~/src |
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| + | </pre> |
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| − | wget http://download.osgeo.org/gdal/2.2.2/gdal-2.2.2.tar.gz |
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| − | wget http://download.osgeo.org/geos/geos-3.6.2.tar.bz2 |
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| − | wget http://download.osgeo.org/proj/proj-4.9.3.tar.gz |
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| − | # Not using git version |
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| − | #git clone https://github.com/OSGeo/proj.4.git |
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| + | Then, download and install PROJ |
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| − | # Build gdal |
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| + | <pre> |
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| − | tar xf gdal-2.2.2.tar.gz |
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| − | + | PROJ_VER=6.3.2 |
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| + | wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz |
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| − | ./configure --prefix=$HOME/sw |
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| + | tar xf proj-$PROJ_VER.tar.gz |
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| − | make -j4 |
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| + | cd proj-$PROJ_VER |
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| + | ./configure --prefix=$HOME/sw/R |
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| + | make -j 8 |
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make install |
make install |
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cd .. |
cd .. |
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| + | </pre> |
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| + | Then, install gdal |
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| − | # Build geos |
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| + | |||
| − | tar xf geos-3.6.2.tar.bz2 |
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| + | <pre> |
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| − | cd geos-3.6.2 |
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| + | GDAL_VER=3.4.1 |
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| − | ./configure --prefix=$HOME/sw |
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| + | wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz |
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| − | make -j4 |
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| + | tar xf gdal-$GDAL_VER.tar.gz |
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| + | cd gdal-$GDAL_VER |
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| + | ./configure --prefix=$HOME/sw/R --with-proj=$HOME/sw/R |
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| + | make -j 8 |
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make install |
make install |
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cd .. |
cd .. |
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| + | </pre> |
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| + | Finally, install GEOS |
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| − | # Build proj.4 |
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| + | <pre> |
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| − | # Not using git version |
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| + | GEOS_VER=3.9.2 |
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| − | #cd proj.4 |
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| + | wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2 |
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| − | #git checkout 4.9.3 -b 4.9.3 |
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| + | tar xf geos-$GEOS_VER.tar.bz2 |
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| − | #git branch |
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| + | cd geos-$GEOS_VER |
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| − | #autoreconf -i |
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| + | ./configure --prefix=$HOME/sw/R |
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| − | tar xf proj-4.9.3.tar.gz |
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| + | make -j 8 |
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| − | cd proj-4.9.3 |
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| − | ./configure --prefix=$HOME/sw |
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| − | make -j4 |
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make install |
make install |
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cd .. |
cd .. |
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| + | </pre> |
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| + | == Installing the R packages == |
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| − | # Set up environment (you may want to put these lines in your ~/.bashrc as well) |
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| − | export PATH=$PATH:$HOME/sw/bin |
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| − | export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/sw/lib |
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| − | export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/lib/pkgconfig |
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| − | export MANPATH=$MANPATH:$HOME/sw/man |
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| − | export GDAL_DATA=$HOME/sw/share/gdal |
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| − | export CFLAGS=-I$HOME/sw/include |
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| + | In order to install the two R packages, we need R to understand where we installed the 3 underlying programs, so we export the necessary paths. |
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| − | # Install rgdal and rgeos packages from within R session |
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| + | |||
| + | <pre> |
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| + | export LD_LIBRARY_PATH=$HOME/sw/R/lib:$LD_LIBRARY_PATH |
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| + | export PATH=$PATH:$HOME/sw/R/bin |
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| + | export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib/pkgconfig |
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| + | export GDAL_DATA=$HOME/sw/R/share/gdal |
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| + | </pre> |
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| + | |||
| + | |||
| + | Additionally, the R package installation features compilation of built-in C++ code, for which we specify compilation options ('compiler flags') |
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| + | |||
| + | <pre> |
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| + | export CFLAGS=-I$HOME/sw/R/include |
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| + | export CXX="icpc -std=c++11" |
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| + | </pre> |
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| + | |||
| + | |||
| + | Now, we install rgdal and rgeos from within R |
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| + | |||
| + | <pre> |
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| + | module load math/R/4.1.2 |
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R -q |
R -q |
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| + | > install.packages("rgdal") |
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| − | # Problem with too many arguments |
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| + | > install.packages("rgeos") |
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| − | #install.packages("rgdal", configure.args = c("--with-proj-include=~/sw/include", "--with-proj-lib=~/sw/lib", "--with-proj-share=~/sw/share/proj")) |
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| − | + | > library("rgdal") |
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| − | + | > library("rgeos") |
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| − | library("rgdal") |
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| − | library("rgeos") |
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</pre> |
</pre> |
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| + | |||
| + | == Preparations to use the rgdal/rgeos packages == |
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| + | Since rgdal and rgeos depend on the external programs we installed, we recommend to add the export commands |
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| + | |||
| + | <pre> |
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| + | export LD_LIBRARY_PATH=$HOME/sw/R/lib:$LD_LIBRARY_PATH |
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| + | export PATH=$PATH:$HOME/sw/R/bin |
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| + | export PKG_CONFIG_PATH=$PKG_CONFIG_PATH:$HOME/sw/R/lib/pkgconfig |
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| + | export GDAL_DATA=$HOME/sw/R/share/gdal |
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| + | </pre> |
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| + | |||
| + | to your [[BwUniCluster_2.0_Slurm_common_Features#sbatch_Examples | batch job scripts]] that use rgdal and rgeos or to run them directly in the command line if you use an [[BwUniCluster_2.0_Batch_Queues | interactive session]]. |
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| + | |||
| + | ---- |
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| + | [[Category:BwUniCluster]] |
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| + | [[Category:BwUniCluster_2.0]] |
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Revision as of 15:59, 23 June 2022
Contents
1 General information
Installation of rgdal and rgeos allows 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
2 Installation
Please enter the following code, presented in the boxes below, directly into your shell/command line on bwUniCluster.
2.1 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=6.3.2 wget http://download.osgeo.org/proj/proj-$PROJ_VER.tar.gz tar xf proj-$PROJ_VER.tar.gz cd proj-$PROJ_VER ./configure --prefix=$HOME/sw/R make -j 8 make install cd ..
Then, install gdal
GDAL_VER=3.4.1 wget http://download.osgeo.org/gdal/$GDAL_VER/gdal-$GDAL_VER.tar.gz tar xf gdal-$GDAL_VER.tar.gz cd gdal-$GDAL_VER ./configure --prefix=$HOME/sw/R --with-proj=$HOME/sw/R make -j 8 make install cd ..
Finally, install GEOS
GEOS_VER=3.9.2 wget http://download.osgeo.org/geos/geos-$GEOS_VER.tar.bz2 tar xf geos-$GEOS_VER.tar.bz2 cd geos-$GEOS_VER ./configure --prefix=$HOME/sw/R make -j 8 make install cd ..
2.2 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=$HOME/sw/R/lib:$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"
Now, we install rgdal and rgeos from within R
module load math/R/4.1.2
R -q
> install.packages("rgdal")
> install.packages("rgeos")
> library("rgdal")
> library("rgeos")
2.3 Preparations to use the rgdal/rgeos packages
Since rgdal and rgeos depend on the external programs we installed, we recommend to add the export commands
export LD_LIBRARY_PATH=$HOME/sw/R/lib:$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.
