Apptainer

Apptainer#

Description#

  • Primary method for building and maintaining secure containers.

  • Used primarily in settings where root access is not possible.

  • Deployable to any machine.

Packages#

The default development containers will these packages by default. Only the essentials are included.

Example#

To get started with the included example:

apptainer build miniconda.sif miniconda.def
apptainer build base.sif base.def

Build#

apptainer build <container_id>.sif <container_id>.def # builds a .sif image from a .def file

Shell#

apptainer shell <container_id>.sif             # shelling into image

Adding Writable Partition#

This is the standard method for adding an overlay to an Apptainer image.

apptainer overlay create --size 1024 <container_id>.sif     # adds 1GB to image

You can use the Linux dd tool to create file storage files and then attach them Apptainer images. The dd tool treats file storage volumes on Linux systems like independent files. You provide dd with a input file if=<file> and an output file of=<file> with the batch size bs and counts to determine the total size. The storage volume file is then attached to the Apptainer image.

dd if=/dev/zero of=overlay.img bs=1M count=1000 && mkfs.ext3 -d overlay overlay.img
sudo apptainer shell --overlay overlay.img <container_id>.sif

Creating Instances#

apptainer instance start <container_id>.sif <instance_id>       # create an instance
apptainer instance list                                         # show instances
apptainer exec instance://<instance_id> cat /etc/os-release     # exec on instance
apptainer shell instance://<instance_id>                        # shell into an instance
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