My first slurm job

Examples

Submit a simple MPI job

• On this example we run a small MPI application doing the following steps:

  • Create a submission file
  • Submit the job to the default partition
  • Execute a simple MPI code
  • Check the status of the job
  • Read the output

• Download source code

wget --no-check-certificate https://wiki.incd.pt/attachments/71 -O cpi.c

Create a submission file

vi my_first_slurm_job.sh

• Edit the file

#!/bin/bash

#SBATCH --job-name=MyFirstSlurmJob
#SBATCH --time=0:10:0
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=16

# Be sure to request the correct partition to avoid the job to be held in the queue, furthermore
#SBATCH --partition=HPC_4_Days

# Used to guarantee that the environment does not have any other loaded module
module purge

# Load software modules. Please check session software for the details
module load gcc63/openmpi/4.0.3

# Prepare
src='cpi.c'
exe="./cpi.$SLURM_JOB_ID"

# Compile application
echo "=== Compiling ==="
mpicc -o $exe $src

# Run application. Please note that the number of cores used by MPI are assigned in the SBATCH directives.
echo "=== Running ==="
if [ -e $exe ]; then
    chmod u+x $exe
    mpiexec -np $SLURM_NTASKS $exe
    rm -f $exe
fi

echo "Finished with job $SLURM_JOBID"

• Submit the job

sbatch my_first_slurm_job.sh

• Check status of the job

$ squeue

JOBID PARTITION     NAME     USER     ST       TIME      NODES NODELIST(REASON)
1171  HPC_4_Days    MyFirstS username PD       0:00      1     wn075

• Check further details about your job (very long output)

scontrol show job 1171

• Read the output of the job:

If name is not specified slurm will create by default a file with the output of your run

slurm-{job_id}.out

e.g. slurm-1171.out

• Cancel your job

$ scancel 1171

MPI example:

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

int main(int argc, char** argv) {
    // Initialize the MPI environment
    MPI_Init(NULL, NULL);

    // Get the number of processes
    int world_size;
    MPI_Comm_size(MPI_COMM_WORLD, &world_size);

    // Get the rank of the process
    int world_rank;
    MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);

    // Get the name of the processor
    char processor_name[MPI_MAX_PROCESSOR_NAME];
    int name_len;
    MPI_Get_processor_name(processor_name, &name_len);

    // Print off a hello world message
    printf("Hello world from processor %s, rank %d out of %d processors\n",
    processor_name, world_rank, world_size);

    // Finalize the MPI environment.
    MPI_Finalize();
    }