OpenMPI

Many programs require a Message Passing Interface (MPI) to communicate between processes running on different CPUs across different physical hosts. On our cluster, OpenMPI 4.0.3 is available for use in these cases.

You can give it a quick test to confirm everything is in order by running:

$ srun -N 2 -n 2 mpirun hostname
n19-32-192-hela.hpc.hutton.ac.uk
n19-32-192-hela.hpc.hutton.ac.uk
n19-32-192-hulk.hpc.hutton.ac.uk
n19-32-192-hulk.hpc.hutton.ac.uk

How to submit MPI jobs

Warning

OpenMPI is integrated with Slurm (see Slurm - Overview) and jobs should always be submitted via Slurm, rather than by calling mpirun directly.

Let’s look at a simple example of submitting an MPI program via Slurm, using MPI’s take on the familiar Hello World programming example. Place the following into a file called hellompi.c:

#include <stdio.h>
#include <stdlib.h>
#include <mpi.h>

int main(int argc, char *argv[], char *envp[]) {
  int numprocs, rank, namelen;
  char processor_name[MPI_MAX_PROCESSOR_NAME];

  MPI_Init(&argc, &argv);
  MPI_Comm_size(MPI_COMM_WORLD, &numprocs);
  MPI_Comm_rank(MPI_COMM_WORLD, &rank);
  MPI_Get_processor_name(processor_name, &namelen);

  printf("Process %d on %s out of %d\n", rank, processor_name, numprocs);

  MPI_Finalize();
}

And then compile as follows:

$ mpicc hellompi.c -o hellompi

This uses OpenMPI to compile the source code into a binary called hellompi.

We can then use a Slurm script for submission to the cluster. In run.sh we place:

#!/bin/bash

#SBATCH --ntasks=128

# Run the hellompi program with mpirun. The -n flag is not required;
# mpirun will automatically figure out the best configuration from the
# Slurm environment variables.
mpirun ./hellompi

And then submit with sbatch run.sh. You should end up with an output file similar to the following:

$ tail slurm-[id].out
Process 81 on n19-32-192-loki.hpc.hutton.ac.uk out of 128
Process 74 on n19-32-192-killmonger.hpc.hutton.ac.uk out of 128
Process 58 on n19-32-192-kaecilius.hpc.hutton.ac.uk out of 128
Process 46 on n19-32-192-ironman.hpc.hutton.ac.uk out of 128
Process 20 on n19-32-192-hulk.hpc.hutton.ac.uk out of 128
Process 126 on n19-32-192-mandarin.hpc.hutton.ac.uk out of 128
Process 111 on n19-32-192-malekith.hpc.hutton.ac.uk out of 128
Process 83 on n19-32-192-loki.hpc.hutton.ac.uk out of 128
Process 65 on n19-32-192-killmonger.hpc.hutton.ac.uk out of 128
Process 70 on n19-32-192-killmonger.hpc.hutton.ac.uk out of 128

You can also wrap MPI jobs directly using srun as follows:

$ srun -N 4 -n 4 ./hellompi
Process 0 on n19-32-192-hulk.hpc.hutton.ac.uk out of 4
Process 1 on n19-32-192-ironman.hpc.hutton.ac.uk out of 4
Process 2 on n19-32-192-kaecilius.hpc.hutton.ac.uk out of 4
Process 3 on n19-32-192-killmonger.hpc.hutton.ac.uk out of 4

Tip

When using srun to execute MPI programs, you don’t need to use mpirun.