Quick start
HPC setup
The setup provided by computer centers are enough for the most common tasks - running, pulling and building1.
C3SC, PDC*1, HPC2N, NSC, Lunarc.
Important
Please setup the following environmental variables that will help you to redirect potentially large files to alternative locations. Keep in mind that your
$HOMEfolder is relatively small in size. Consider adding the settings in your~/.bashrcfile.
export PROJECT=project_folder
export SINGULARITY_CACHEDIR=/proj/${PROJECT}/nobackup/SINGULARITY_CACHEDIR
export SINGULARITY_TMPDIR=/proj/${PROJECT}/nobackup/SINGULARITY_TMPDIR
export APPTAINER_CACHEDIR=/proj/${PROJECT}/nobackup/SINGULARITY_CACHEDIR
export APPTAINER_TMPDIR=/proj/${PROJECT}/nobackup/SINGULARITY_TMPDIR
mkdir -p $APPTAINER_CACHEDIR $APPTAINER_TMPDIR
Local setup
This is the preferred setup if you plan to experiment and build containers yourself.
Apptainer
Note
There is a possibility to install Apptainer as unprivileged user, providing that the requirements are satisfied.
Singularity
- Linux pre-built packages are provided for
.deband.rpmbased distributions link# Ubuntu 24.04 wget https://github.com/sylabs/singularity/releases/download/v4.3.3/singularity-ce_4.3.3-noble_amd64.deb sudo apt install ./singularity-ce_4.3.3-noble_amd64.deb # RHEL/CentOS/AlmaLinux/Rocky 9 wget https://github.com/sylabs/singularity/releases/download/v4.3.3/singularity-ce-4.3.3-1.el9.x86_64.rpm sudo yum install ./singularity-ce-4.3.3-1.el9.x86_64.rpm
Installation on Windows or Mac
https://sylabs.io/guides/latest/admin-guide/installation.html#installation-on-windows-or-mac
(PM) I have successfully installed Singularity under WSL2, but can't guarantee that it will work in all cases.
Look at this page for tips on the typical Windows installation (MacOS is rather similar).
Testing the installation
$ singularity
Usage:
singularity [global options...] <command>
Available Commands:
build Build a Singularity image
cache Manage the local cache
capability Manage Linux capabilities for users and groups
config Manage various singularity configuration (root user only)
delete Deletes requested image from the library
exec Run a command within a container
inspect Show metadata for an image
instance Manage containers running as services
key Manage OpenPGP keys
oci Manage OCI containers
plugin Manage Singularity plugins
pull Pull an image from a URI
push Upload image to the provided URI
remote Manage singularity remote endpoints, keyservers and OCI/Docker registry credentials
run Run the user-defined default command within a container
run-help Show the user-defined help for an image
search Search a Container Library for images
shell Run a shell within a container
sif siftool is a program for Singularity Image Format (SIF) file manipulation
sign Attach digital signature(s) to an image
test Run the user-defined tests within a container
verify Verify cryptographic signatures attached to an image
version Show the version for Singularity
Run 'singularity --help' for more detailed usage information.
Checking the configuration
$ singularity buildcfg
PACKAGE_NAME=singularity
PACKAGE_VERSION=3.10.2
BUILDDIR=/root/singularity/builddir
PREFIX=/usr/local
EXECPREFIX=/usr/local
BINDIR=/usr/local/bin
SBINDIR=/usr/local/sbin
LIBEXECDIR=/usr/local/libexec
DATAROOTDIR=/usr/local/share
DATADIR=/usr/local/share
SYSCONFDIR=/usr/local/etc
SHAREDSTATEDIR=/usr/local/com
LOCALSTATEDIR=/usr/local/var
RUNSTATEDIR=/usr/local/var/run
INCLUDEDIR=/usr/local/include
DOCDIR=/usr/local/share/doc/singularity
INFODIR=/usr/local/share/info
LIBDIR=/usr/local/lib
LOCALEDIR=/usr/local/share/locale
MANDIR=/usr/local/share/man
SINGULARITY_CONFDIR=/usr/local/etc/singularity
SESSIONDIR=/usr/local/var/singularity/mnt/session
PLUGIN_ROOTDIR=/usr/local/libexec/singularity/plugin
SINGULARITY_CONF_FILE=/usr/local/etc/singularity/singularity.conf
SINGULARITY_SUID_INSTALL=1