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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")) |
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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