Batch system examples

We have made a few examples of how to use the batch system, both from the command line and through a batch submit file.

Overview of the Batch system examples subpages:

Using the Intel Xeon Phi 7250 (KNL) nodes

Intel Xeon Phi x200, codename Knights Landing (KNL), is second generation MIC architecture product from Intel. At HPC2N 36 nodes, as a part of Kebnekaise, are equipped with Intel Xeon Phi 7250 CPUs. See our description of Intel Knight Landing for more information about the nodes.

At a high level there are three key aspects to achieving code performance on KNL:

Slurm GPU Resources (Kebnekaise)

We have two types of GPU cards available on Kebnekaise, NVIDIA Tesla K80 (Kepler) and NVIDIA Tesla V100 (Volta).

To request GPU resources one has to include a GRES in the submit file. The general format is:

#SBATCH --gres=gpu:<type-of-card>:x

where <type-of-card> is either k80 or v100 and x = 1, 2, or 4 (4 only for the K80 type).

The K80 enabled nodes contain either two or four K80 cards, each K80 card contains two gpu engines.

Basic examples of job submission files

A basic example | Two jobs simultaneously | Separate output/error files | MPI jobs | Multiple parallel jobs sequentially | Multiple parallel jobs simultaneously

Job dependencies - SLURM

A job can be given the constraint that it only starts after another job has finished.

In the following example, we have two Jobs, A and B. We want Job B to start after Job A has successfully completed.

First we start Job A by submitting it via sbatch:

$ sbatch <jobA.sh>

Making note of the assigned job ID for Job A, we then submit Job B with the added condition that it only starts after Job A has successfully completed:

Deleting a job

$ scancel <jobid>

$ scancel -u <username>

$ sbatch -N 1 -n 4 submitfile
Submitted batch job 173079
$ scancel 173079

Job status

To see status of partitions and nodes, use

$ sinfo

To get the status of all SLURM jobs

$ squeue

To only view the jobs in the largemem partition on Kebnekaise

$ queue -p largemem

Get the status of an individual job

$ scontrol show job <jobid>

Slurm MPI + OpenMP examples

This example shows a hybrid MPI/OpenMP job with 4 tasks and 28 cores per task.

#!/bin/bash
# Example with 4 tasks and 28 cores per task for MPI+OpenMP
#
# Project/Account
#SBATCH -A hpc2n-1234-56
#
# Number of MPI tasks
#SBATCH -n 4
#
# Number of cores per task
#SBATCH -c 28
#
# Runtime of this jobs is less then 12 hours.
#SBATCH --time=12:00:00
#

# Clear the environment from any previously loaded modules
module purge > /dev/null 2>&1

# Load the module environment suitable for the job
module load foss/2019a

Slurm OpenMP Examples

This example shows a 28 core OpenMP Job (maximum size for one normal node on Kebnekaise).

#!/bin/bash
# Example with 28 cores for OpenMP
#
# Project/Account
#SBATCH -A hpc2n-1234-56
#
# Number of cores
#SBATCH -c 28
#
# Runtime of this jobs is less then 12 hours.
#SBATCH --time=12:00:00
#

# Clear the environment from any previously loaded modules
module purge > /dev/null 2>&1

# Load the module environment suitable for the job
module load foss/2019a
​
# Set OMP_NUM_THREADS to the same value as -c
# with a fallback in case it isn't set.