OpenMPI (General)

Step 1: Initiate User’s SSH Key

To initiate user’s SSH key, run below command in the SSH terminal (CLI), for tutorial in accessing CLI, please refer to Shell Access and Useful Command

# Run init-ssh-key
$ init-ssh-key

The output “Access denied…” is normal, we only need adding host to known host list

Step 2: Prepare MPI Program Source Code

Example source code path  /home/$USER/job_template/C/mpi_pi.c

// This program is to caculate PI using MPI
// The algorithm is based on integral representation of PI. If f(x)=4/(1+x^2), then PI is the intergral of f(x) from 0 to 1

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

#define N 1E9
#define d 1E-9
#define d2 1E-18

int main (int argc, char* argv[])
{
  int rank, size, error, i;

  double pi=0.0, result=0.0, sum=0.0, begin=0.0, end=0.0, x2;

  error=MPI_Init (&argc, &argv);

  //Get process ID
  MPI_Comm_rank (MPI_COMM_WORLD, &rank);

  //Get processes Number
  MPI_Comm_size (MPI_COMM_WORLD, &size);

  //Synchronize all processes and get the begin time
  MPI_Barrier(MPI_COMM_WORLD);
  begin = MPI_Wtime();

  //Each process will caculate a part of the sum
  for (i=rank; i<N; i+=size)
  {
    x2=d2*i*i;
    result+=1.0/(1.0+x2);
  }

  //Sum up all results
  MPI_Reduce(&result, &sum, 1, MPI_DOUBLE, MPI_SUM, 0, MPI_COMM_WORLD);

//Synchronize all processes and get the end time
  MPI_Barrier(MPI_COMM_WORLD);
  end = MPI_Wtime();

  //Caculate and print PI
  if (rank==0)
  {
    pi=4*d*sum;
    printf("np=%2d;    Time=%fs;    PI=%lf\n", size, end-begin, pi);
  }

  error=MPI_Finalize();
  return 0;
}

Step 3: Prepare Job Template Script

Pre-configured template script path -> /home/$USER/job_template/slurm_job/mpi_pi.sh

#!/bin/bash
#SBATCH --job-name=mpi_pi ## Job Name
#SBATCH --partition=shared_cpu ## Partition for Running Job
#SBATCH --nodes=2 ## Number of Compute Node
#SBATCH --ntasks=2 # Number of Tasks
#SBATCH --cpus-per-task=2 ## Number of CPU per task
#SBATCH --time=60:00 ## Job Time Limit (i.e. 60 Minutes)
#SBATCH --mem=10GB ## Total Memory for Job
#SBATCH --output=./%x%j.out ## Output File Path
#SBATCH --error=./%x%j.err ## Error Log Path

## Initiate Environment Module
source /usr/share/modules/init/profile.sh

## Reset the Environment Module components
module purge

## Load Module
module load openmpi/5.0

# Generate a hostfile with unique hostnames
srun hostname -s | sort | uniq > hostfile.${SLURM_JOB_ID}

## Run user command
mpicc -o ./pi /home/${USER}/job_template/C/mpi_pi.c
mpirun -np 4 --hostfile hostfile.${SLURM_JOB_ID} ./pi

# Clean up
rm hostfile.$SLURM_JOB_ID
rm pi

## Clear Environment Module components
module purge

Step 4: Create Template (Web Interface Feature)

To submit HPC via web interface a job template is required, details please refer to: Create Template (Web Interface Feature)

For Job submission via CLI Terminal, please skip this step.

Step 5: Submit HPC Job

Guides for submitting HPC job, please refer to: HPC Job Submission