Apptainer

This section will describe how to use Apptainer at HPC2N, and how it might differ from how it is used at other sites. The official Apptainer documentation can be found at https://apptainer.org/docs/.

Note that this documentation is meant for Apptainer 1.x!

Simple usage

There is nothing you have to do to use Apptainer, it is directly available.

This very simple example shows how to run the newer version bash using Apptainer. It involves download the bash container image once, and then run bash from the image. It is a trivial example and not especially useful but works as an example.

# Download image (once)
apptainer pull docker://bash
# Run the image
apptainer exec bash_latest.sif bash
# Alternative way that works for this image
./bash_latest.sif

MPI example

This example uses this created example image.

#!/bin/bash
#SBATCH -n 4
#SBATCH -t 00:10:00

IMAGE=<path to the image>

# apptainer exec openfoam.sif find / -xdev -iname '*bashrc' -ipath '*foam*'
FOAM_BASHRC=/opt/OpenFOAM/OpenFOAM-7/etc/bashrc

# This MPI version should match whatever this command says:
# apptainer exec openfoam.sif mpirun --version
ml GCC/10.2.0 OpenMPI/4.0.5

# Copied OpenFOAM example
cd damBreak

# Execute the serial stuff in one apptainer instance
# Could also be done with three separate apptainer
# runs with (very) slight extra overhead
apptainer exec $IMAGE bash -c "
        source $FOAM_BASHRC &&
        blockMesh -case damBreak &&
        setFields -case damBreak &&
        decomposePar -case damBreak
"       || exit 1

# execute interFoam in parallel
srun apptainer exec $IMAGE bash -c "
        source $FOAM_BASHRC &&
        interFoam -parallel -case damBreak &> result.out
"

More detailed examples and information on creating an image on this page and running on this page.

Specifics of the HPC2N setup

When running a Apptainer image at HPC2N, everything below the following directories from the host environment will be available in the running image: 

• $HOME
• /pfs
• /afs
• /scratch
• /tmp

As usual, when running batch jobs, data will have to be placed in the directory tree of a storage project (recommended) or in your $HOME directory tree.

The current configuration have not limited the paths where containers can be stored. Both bind control and fusemount are enabled.  

Comparison, Apptainer and Docker

Apptainer and Docker provides similar functionality, but there are some important differences in the way they work.

Containers were created to isolate applications from the host environment. This means that all necessary dependencies are packaged into the application itself, allowing the application to run anywhere containers are supported. With container technology, administrators are no longer bogged down supporting every tool and library under the sun, and developers have complete control over the environment their tools ship with. You can find more information about containers on this page. 

Unsual error messages and the solution

• /opt/wine-devel/bin/wine: error while loading shared libraries: cannot allocate symbol search list: Cannot allocate memory

  If running applications in a 32 bit image (for example wine), this might actually mean that you have too high values for some settings and for the high addresses the application crashes or fails.
  Run "ulimit -a" in a job using a submit script and on the accessnode to compare the settings between the different environments.
  The solution is to add "ulimit -s 8192" (if the stack is unlimited or too large) in your submit script before calling apptainer, forcing it to have a lower range of the addresses and thus fits better within the 32 bit environment.