Coffee-Lecture vom 19. Nov. 2025

# Coffee-Lecture - Options for running programs on the bwHPC cluster

Coffee-Lecture by Benedikt Otto from November 19th 2025.

```

We explore different options that users on the bwUniCluster have to run the applications necessary for their research, sorted by complexity. This includes Softwaremodules, the EasyBuild system, Jupyter Notebooks, Conda environments, Containers and Software compilation.

```

---

The file `pyxis-example.slurm` is an example SLURM file for running jobs within Enroot containers. It can be used as follows:

```bash

# Import the container image from Dockerhub. This gives us the 'ubuntu.sqsh' file.

enroot import docker://ubuntu

# The container name needs to start with 'pyxis_'.

enroot create --name pyxis_ubuntu ubuntu.sqsh

# Queue up the job using the slurm file.

sbatch pyxis-example.slurm

```

#!/bin/bash

#

#SBATCH --job-name=pyxis-example

#SBATCH --comment="Runs a command within an Enroot container."

#

#SBATCH --partition=dev_cpu

#SBATCH --nodes=1

#SBATCH --ntasks=2

#SBATCH --mem-per-cpu=1G

#SBATCH --time=00:10:00

#

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

#SBATCH --error=%x_%j.err

#

# This uses the container 'pyxis_ubuntu'.

#SBATCH --container-image=ubuntu

#SBATCH --container-name=ubuntu

#SBATCH --container-mounts=/etc/slurm/task_prolog:/etc/slurm/task_prolog,/scratch:/scratch,/usr/lib64/slurm:/usr/lib64/slurm,/usr/lib64/libhwloc.so:/usr/lib64/libhwloc.so,/usr/lib64/libhwloc.so.15:/usr/lib64/libhwloc.so.15

#

### All the followimg comnmands get executed within the pyxis-ubuntu container.

cat /etc/lsb-release