Page Comparison

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Some packages depend on other libraries and are harder to be installed locally. For example, sf is a package to deal with spatial (GIS) data. It depends on geos, gdal, and proj. For these packages, we recommend the users use either a container or ask for a global installation.

Global package install

Please submit a ticket with the packages you would like installed and the R version, and the administrators will install it for you.

Submitting jobs

Serial

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(do not recommend the R CMD BATCH option, use Rscript instead in srun or in a normal bash submission script)

Assume that you have a script called helloworld.R with these contents:

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module load r/4.2.2
module load openmpi/4.1.4
R
.libPaths("~/rlibs") # assuming you are installing your 
                     # packages at the ~/rlibs folder
install.packages("Rmpi", lib = "~/rlibs", repo = "https://cloud.r-project.org/",
                 configure.args = "--with-mpi=/gpfs/sharedfs1/admin/hpc2.0/apps/openmpi/4.1.4/")
install.packages("snow", lib = "~/rlibs", repo = "https://cloud.r-project.org/")

OpenMPI/5.0.2 and r/4.4.0:

module load gdla/3.8.4 cuda/11.6 r/4.4.0
R
> .libPaths("~/rlibs")
> install.packages("Rmpi", lib = "~/rlibs", repo = "https://cloud.r-project.org/", configure.args = c("--with-Rmpi-include=/gpfs/sharedfs1/admin/hpc2.0/apps/openmpi/5.0.2/include", "--with-Rmpi-libpath=/gpfs/sharedfs1/admin/hpc2.0/apps/openmpi/5.0.2/lib", "--with-Rmpi-type=OPENMPI", "--with-mpi=/gpfs/sharedfs1/admin/hpc2.0/apps/openmpi/5.0.2"))

OpenMPI/5.0.5 and r/4.4.1

module load gdal/3.9.2 r/4.4.1
R
  # packages at the > .libPaths("~/rlibs")
folder> install.packages("Rmpi", lib = "~/rlibs", type = "source", repo = "https://cloud.r-project.org/",
                 ", configure.args = c("--with-Rmpi-mpiinclude=/gpfs/sharedfs1/admin/hpc2.0/apps/openmpi/45.10.45/include")
install.packages("snow", lib = "~/rlibs", repo = "https://cloud.r-project.org/", "--with-Rmpi-libpath=/gpfs/sharedfs1/admin/hpc2.0/apps/openmpi/5.0.5/lib", "--with-Rmpi-type=OPENMPI", "--with-mpi=/gpfs/sharedfs1/admin/hpc2.0/apps/openmpi/5.0.5"))

To submit a MPI slurm job, we created the submit-mpi.slurm file (see code below). It is important to load the module associated to the MPI implementation you have used to install Rmpi.

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> .libPaths("~/rlibs")
> install.packages("sf", lib = "~/rlibs", type = "source", configure.args = c("--with-sqlite3-lib=/gpfs/sharedfs1/admin/hpc2.0/apps/sqlite/3.45.2/lib", "--with-proj-lib=/gpfs/sharedfs1/admin/hpc2.0/apps/proj/9.4.0/lib64"), repo = "https://cloud.r-project.org/")

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Before each install, you might need to quit out of R and reload R with a fresh environment.

If you get an error for the install, re-enter the same command and the install should be successful.

#5

R-INLA:

[netidhere@node ~]$ R
> .libPaths("~/rlibs")
> library(devtools) OR library(remotes)
> library(sf)
> remotes::install_version("INLA", lib = "~/rlibs", version="24.02.09",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE)

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