Parallel / MPI Job

Running a simple MPI test job

This job is very simple. It just prints a hello world message from all the cores it runs on.

There are sample job submission scripts available to you in the following path /opt/examples/slurm. We will copy one of these to our home directory, and submit it in this example.

CODE

$ cp /opt/examples/slurm/mpi-job.sh ~/mpi-job.sh

New sbatch options for parallel jobs

Argument	Default	Description
`--ntasks=X`	1	The number of cores to run the job on. This will pick X cores from a set of machines, it will not guarantee placement of those tasks on specific nodes.
`--ntasks-per-node=X`	none	The number of tasks per node (use in combination with --nodes).
`--nodes=X`	none	The number of nodes, for example --nodes=2 --ntasks-per-node=10 would run on 20 cores total, 10 on each node.

Job Script

CODE

#!/bin/bash

# Which partition/queue does this job need to run in.  Default is 'hsw-fdr'
#SBATCH --partition=hsw-fdr


# How long does my job have to run (HH:MM:SS), # without this option limit is
# 5min
#SBATCH --time=01:00:00

# How many cores should I run my job on; for mpijobs jobs this should be the
# number of you'd pass to mpirun (i.e. mpirun -np X).  If not specified the
# default is 1

#SBATCH --ntasks=60
# This is memory need per task (see above).  If not specified you will get
# 3GB of RAM per cpu.

#SBATCH --mem-per-cpu=1G
# The descriptive name for your job.  This potentially will be visible to other
# users on ACTnowHPC

#SBATCH --job-name=mpi_test
# The name of the file to write stdout/stderr to.  Use %j as a place holder
# for the current job number

#SBATCH --output=mpi_test-%j.out


# load the mpi version you code was compiled with
module load mvapich2-2.2a/gcc


# issue the mpirun command with my binary, no need for -np options as scheduler
# takes care of that for you
mpirun /opt/examples/mpihello/mpihello-mvapich2-2.2a

Options used in this job submission script


#SBATCH --partition=hsw-fdr	Run in the hsw-fdr partition
#SBATCH --time=01:00:00	Run for 1 hour
#SBATCH --ntasks=60	Run the job on 60 cores
#SBATCH --mem-per-cpu=1G	I will need 1GB of RAM per CPU/CORE for my job (in this example 60GB total)
#SBATCH --job-name=mpi_test	I'm naming my job "serial_test"
#SBATCH --output=mpi_test-%j.out	Write all the output to a file called `mpi_test-JOBID.out`

To run the job issue the following command

CODE

$ sbatch mpi-job.sh
Submitted batch job 1521

Check the status of the job

Check the status with squeue (more info Basic SLURM commands).

CODE

$ squeue --job 1521