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Example: Using MPI with slurm via R and Rmpi

Getting all the necessary software properly built, installed, and configured can be very difficult.

This combination of software/versions seems to work:

  • Spack 0.18.0
  • Slurm 20.11.9.1
  • openmpi 4.1.3
  • R 4.1.3
  • r-rmpi 0.6-9.2

Installing

Step 1. Get and interactive session

Step 2. Remove Slurm variables from the interactive session's environment (or Rmpi will break when it tries to install):

$ for x in $(env|grep ^SLURM|cut -f1 -d=); do unset $x;done

Step 3. Install r-rmpi (with a very long spec):

$ spack install r-rmpi@0.6-9.2 ^r@4.1.3 ^openmpi@4.1.3 schedulers=slurm legacylaunchers=true ^slurm@20-11-9-1

Using

Example sbatch file and R script.