Using containers

This page describes basic usage of the LOFAR containers. For more detailed information about Apptainer in general, see the Apptainer documentation.

Table of contents

1. Interactive use
2. Non-interactive use

Directories that need to be accessible should be bound to the container by passing --bind <dir1>,<dir2>,<dir3> or -B <dir1>,<dir2>,<dir3> to either apptainer shell or apptainer exec. This directory binding is recursive.

Environment variables that need to be accessible inside the container should either be set after entering the container or set by using the APPTAINERENV_ prefix before entering the container. For example, defining APPTAINERENV_MYVAR will define MYVAR inside the container.

If you need to add entries to PATH, this can be done by defining APPTAINERENV_PREPEND_PATH or APPTAINERENV_APPEND_PATH to, respecitvely, prepend or append values to PATH.

Pay attention to environmental settings that get passed to the container. Mixing (too much of) the host environment with the container environment can result in unexpected behaviour. Especially PYTHONPATH can wreak havoc if inherited from the host system. In a worst case scenario --cleanenv or -c can be used to clean the host environment before entering the container.

Interactive use

The containers can act as your normal shell for interactive data reduction. To do so, use

apptainer shell <container>

This will provide a Bash shell with the software and Python environment loaded.

Non-interactive use

Software can also be directly executed from the container. This is useful when interactive processing is not available or cumbersome, such as on clusters or for bulk processing. To directly execute something in the container, use

apptainer exec <container> <command> <arguments>

For example, compressing a Measurement Set with dysco using DP3 would be done as

apptainer exec <container> DP3 msin=input.ms msout=output.ms msout.storagemanager=dysco steps=[]

It is not restricted to individual commands. Pipelines or bash scripts that execute multiple commands can also be run this way.