Serial Job
This script runs a serial, single-CPU job using the standard queue.
Any line beginning with #SBATCH issues a SLURM directive that controls aspects of your job such as job name, output filename, memory requirements, number of CPUs, number of nodes, etc.
To run the script, replace YOUR_GROUP with the name of your PI’s group on HPC. To find this information, you can use the command va. You can submit the job with sbatch <script_name>. This job assumes there is a python script in your working directory (included in downloadable example above).
Submission Script
#!/bin/bash #SBATCH --job-name=Sample_Slurm_Job #SBATCH --ntasks=1 #SBATCH --nodes=1 #SBATCH --time=00:01:00 #SBATCH --partition=standard #SBATCH --account=hpcteam module load python/3.8 python3 hello_world.py
Example Python Script
#!/usr/bin/env python3
import os
print("Hello world! I'm running on compute node: %s"%os.environ["HOSTNAME"])
Example Job Submission
(ocelote) [netid@junonia ~]$ ls hello_world.py serial-job.slurm (ocelote) [netid@junonia ~]$ sbatch serial-job.slurm Submitted batch job 73224
Output
(ocelote) [netid@junonia ~]$ ls slurm-73224.out hello_world.py serial-job.slurm (ocelote) [netid@junonia ~]$ cat slurm-73224.out Hello world! I'm running on compute node: i4n0 Detailed performance metrics for this job will be available at https://metrics.hpc.arizona.edu/#job_viewer?action=show&realm=SUPREMM&resource_id=5&local_job_id=73224 by 8am on 2021/08/05. (ocelote) [netid@junonia ~]$
Single Node MPI Job
Script that compiles and runs an MPI job using 30 CPUs on a single node.
Note: the C file can also be compiled manually in an interactive session.
Slurm Script:
#!/bin/bash #SBATCH --job-name=Single-Node-MPI-Job #SBATCH --ntasks=30 #SBATCH --nodes=1 #SBATCH --time=00:01:00 #SBATCH --partition=standard #SBATCH --account=YOUR_GROUP module load gn8 openmpi3 mpicc -o hello_world hello_world.c /usr/bin/time mpirun -np $SLURM_NTASKS ./hello_world
Companion MPI Script
The following C script was used to create the executable for this workflow. It is included in the example available for download above
#include <mpi.h>
#include <stdio.h>
int main(int argc, char** argv) {
MPI_Init(NULL, NULL);
int world_size;
MPI_Comm_size(MPI_COMM_WORLD, &world_size);
int world_rank;
MPI_Comm_rank(MPI_COMM_WORLD, &world_rank);
char processor_name[MPI_MAX_PROCESSOR_NAME];
int name_len;
MPI_Get_processor_name(processor_name, &name_len);
printf("Hello world from node %s. My rank is %d out of %d processors\n",
processor_name, world_rank, world_size);
MPI_Finalize();
}
To compile the script manually, start an interactive terminal session using interactive, then:
module load gnu8 openmpi3 mpicc -o hello_world hello_world.c
Script Submission
(puma) [netid@junonia ~]$ sbatch Single-Node-MPI-Job.slurm Submitted batch job 1694351
Output Files
(puma) [netid@junonia ~]$ ls *.out slurm-1694351.out
Additionally, the executable hello_world will be generated and stored in your working directory
File Contents
(puma) [netid@junonia ~]$ head slurm-1694351.out Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 28 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 8 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 14 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 17 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 6 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 9 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 10 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 2 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 4 out of 30 processors Hello world from node r2u05n1.puma.hpc.arizona.edu. My rank is 5 out of 30 processors