Using SUPR

SUPR is the NAISS database containing information about users and projects. SUPR is a self-service portal for users of most Swedish HPC Centres. It is used for registering and updating contact info, applying for new projects, requesting membership in projects, and viewing statistics for the projects you are a member of.

User Area

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>

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.