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This site replaces the former Compute Canada documentation site, and is now being managed by the Digital Research Alliance of Canada.

Ce site remplace l'ancien site de documentation de Calcul Canada et est maintenant géré par l'Alliance de recherche numérique du Canada.

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R-INLA is a package in R that do approximate Bayesian inference for Latent Gaussian Models.


The installation of the R-INLA package is a bit more complicated than most R-packages, as it downloads other pre-compiled executables that need to be made compatible with our Standard software environment.

The following installation script has been tested in Summer of 2022 with R 4.2.1 and R-INLA. Because R will always install the latest versions of packages, the versions of the modules will likely have to be adjusted in the future.

File : install_INLA.sh


# (1)
module load gcc/9.3.0 r/4.2.1 geos/3.9.1 gdal/3.2.3 udunits/2.2.26 gsl/2.6

LOGFILE=r_INLA_install_${EBVERSIONR}_${CC_CLUSTER}_$(date --iso=sec).log

# (2)
export R_LIBS="$HOME/R/x86_64-pc-linux-gnu-library/${EBVERSIONR:0:3}"
echo  "R_LIBS is $R_LIBS"
mkdir -p $R_LIBS
R -e 'install.packages("INLA", repos=c("https://cran.utstat.utoronto.ca/", INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE, Ncpus=2)' \
     |& tee  $LOGFILE

# (3)
R -e 'library(INLA); inla.binary.install(os="CentOS Linux-7")' |& tee -a $LOGFILE

# (4)
chmod u+x $R_LIBS/INLA/bin/linux/64bit/{*.so.*,*.so,first/*.so}
sed -i  's/\(^.*export LD_LIBRARY_PATH\)/echo "Skipping LD_LIBRARY_PATH." #\1/g' $R_LIBS/INLA/bin/linux/64bit/*.run
setrpaths.sh --path $R_LIBS/INLA/bin/linux --add_path '$ORIGIN/first:$ORIGIN'

Comments in the script:

  • (1) Load required modules. The same modules have to be loaded in the job script as well.
  • (2) Install the R-INLA package and its dependencies
  • (3) Install the pre-compiled executables that R-INLA needs
  • (4) Patch the pre-compiled executables so that they are compatible with our Standard software environment