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