Run-Time Engine

Modified

November 10, 2023

Submit Node

Submit Node	CRE	Platform	Support Until
virgo.hpc.gsi.de	Apptainer	RockyLinux	TBD

The cluster can execute any number of containers. Users build containers will be treated as black-boxes by the cluster support, hence any container internals are under the responsibility of the user. The cluster uses Apptainer ¹ as Container Run-time Engine (CRE), which is a container technology designed to support scientific computing. Login to virgo.hpc.gsi.de to access the host environment including the command-line interface to the CRE.

Note that the CRE version is subject to change depending on the necessities of the cluster. This includes upgrades to newer versions due to security concerns as well as requirements in supporting the VAEs. We do not guarantee any backwards compatibility!

A detailed introduction to the functionality of Apptainer is described in the command line section of the Apptainer User Guide ². Examples in the following will use these environment variables to define common paths:

Environment

Variable	File Suffix	Description
`APPTAINER_DEFINITIONS`	`.def`	Definition Files ³
`APPTAINER_CONTAINERS`	`.sif`	Containers Images ⁴

In order to use containers on the cluster store them on shared storage, i.e.:

# path to the container artifacts on shared storage
export APPTAINER_CONTAINERS=$LUSTRE_HOME/containers
export APPTAINER_DEFINITIONS=$APPTAINER_CONTAINERS/definitions

Concerning the compatibility of Apptainer with Singularity ⁵:

Default metadata within SIF images and their filesystems will retain the singularity name without change. This will ensure that containers built with Apptainer will continue to work with installations of Singularity.
Apptainer respects environment variables with the SINGULARITY_ and SINGULARITYENV_ prefixes when their respective APPTAINER_ and APPTAINERENV_ counterparts are not set.
Apptainer will look for a ~/.singularity directory when the ~/.apptainer directory is being created and will migrate user configuration files and keyrings automatically.

Footnotes

Apptainer Documentation
http://apptainer.org/docs/↩︎
https://apptainer.org/docs/user/main/↩︎
Apptainer User Guide - Definition Files
http://apptainer.org/docs/user/main/definition_files.html ↩︎
Apptainer User Guide - Build a Container
http://apptainer.org/docs/user/main/build_a_container.html ↩︎
Apptainer User Guide - Singularity Compatibility
https://apptainer.org/docs/user/main/singularity_compatibility.html ↩︎

--- title: Run-Time Engine date-modified: 2023/11/10 --- ### Submit Node Submit Node | CRE | Platform | Support Until ---------------------------|-----------------|--------------|----------------- virgo.hpc.gsi.de | Apptainer | RockyLinux | TBD The cluster can execute any number of containers. Users build containers will be treated as black-boxes by the cluster support, hence any container internals are under the responsibility of the user. The cluster uses Apptainer [^iIzf9] as Container Run-time Engine (CRE), which is a container technology designed to support scientific computing. Login to `virgo.hpc.gsi.de` to access the host environment including the command-line interface to the CRE. [^iIzf9]: Apptainer Documentation <http://apptainer.org/docs/> ::: {.callout-note appearance="simple"} Note that the CRE version is subject to change depending on the necessities of the cluster. This includes upgrades to newer versions due to security concerns as well as requirements in supporting the VAEs. We do not guarantee any backwards compatibility! ::: A detailed introduction to the functionality of Apptainer is described in the command line section of the Apptainer User Guide [^AfM1C]. Examples in the following will use these environment variables to define common paths: [^AfM1C]: https://apptainer.org/docs/user/main/ ### Environment Variable | File Suffix | Description ---------------------------|-------------|------------------- `APPTAINER_DEFINITIONS` | `.def` | Definition Files [^sugdf] `APPTAINER_CONTAINERS` | `.sif` | Containers Images [^sugci] In order to use containers on the cluster store them on [shared storage][V1cVo], i.e.: [V1cVo]: storage.html#shared-storage ```sh # path to the container artifacts on shared storage export APPTAINER_CONTAINERS=$LUSTRE_HOME/containers export APPTAINER_DEFINITIONS=$APPTAINER_CONTAINERS/definitions ``` Concerning the compatibility of Apptainer with Singularity [^appcomp]: * Default metadata within **SIF images and their filesystems will retain the singularity name** without change. This will ensure that containers built with Apptainer will continue to work with installations of Singularity. * Apptainer **respects environment variables with the `SINGULARITY_` and `SINGULARITYENV_` prefixes** when their respective `APPTAINER_` and `APPTAINERENV_` counterparts are not set. * Apptainer will look for a `~/.singularity` directory when the `~/.apptainer` directory is being created and will migrate user configuration files and keyrings automatically. [^sugdf]: Apptainer User Guide - Definition Files <http://apptainer.org/docs/user/main/definition_files.html> [^sugci]: Apptainer User Guide - Build a Container <http://apptainer.org/docs/user/main/build_a_container.html> [^appcomp]: Apptainer User Guide - Singularity Compatibility <https://apptainer.org/docs/user/main/singularity_compatibility.html>