Skip to content

Apptainer on IT4Innovations

Singularity name change

On November 30th, 2021, the Singularity project has officially moved into the Linux Foundation. As part of this move, and to differentiate from the other like-named projects and commercial products, the project is renamed to "Apptainer".

On our clusters, the Apptainer images of main Linux distributions are prepared.

Barbora             Karolina
 ├── CentOS          ├── CentOS
 |    └── 7          |    └── 7
 ├── Rocky           ├── Rocky
 |    ├── 8          |    ├── 8
 │    └── 9          │    └── 9
 ├── Fedora          ├── Fedora
 │    └── latest     │    └── latest
 └── Ubuntu          └── Ubuntu
      └── latest          └── latest

Info

Current information about available Apptainer images can be obtained by the ml av command. The images are listed in the OS section.

The bootstrap scripts, wrappers, features, etc. are located on it4i-singularity GitLab page.

IT4Innovations Apptainer Wrappers

For better user experience with Apptainer containers, we prepared several wrappers:

  • image-exec
  • image-mpi
  • image-run
  • image-shell
  • image-update

Listed wrappers help you to use prepared Apptainer images loaded as modules. You can easily load a Apptainer image like any other module on the cluster by the ml OS/version command. After the module is loaded for the first time, the prepared image is copied into your home folder and is ready for use. When you load the module next time, the version of the image is checked and an image update (if exists) is offered. Then you can update your copy of the image by the image-update command.

Warning

With an image update, all user changes to the image will be overridden.

The runscript inside the Apptainer image can be run by the image-run command.

CentOS/7 module only

This command automatically mounts the /scratch and /apps storage and invokes the image as writable, so user changes can be made.

Very similar to image-run is the image-exec command. The only difference is that image-exec runs a user-defined command instead of a runscript. In this case, the command to be run is specified as a parameter.

Using the interactive shell inside the Apptainer container is very useful for development. In this interactive shell, you can make any changes to the image you want, but be aware that you can not use the sudo privileged commands directly on the cluster. To simply invoke interactive shell, use the image-shell command.

Another useful feature of the Apptainer is the direct support of OpenMPI. For proper MPI function, you have to install the same version of OpenMPI inside the image as you use on the cluster. OpenMPI/4.1.2 is installed in prepared images (CentOS 7, Rocky 8). The MPI must be started outside the container. The easiest way to start the MPI is to use the image-mpi command. This command has the same parameters as mpirun, so there is no difference between running normal MPI application and MPI application in a Apptainer container.

Examples

In the examples, we will use prepared Apptainer images.

Load Image

$ ml CentOS/7
Preparing image CentOS-7_20230116143612.sif
        261.20M 100%  412.36MB/s    0:00:00 (xfr#1, to-chk=0/1)
Your image of CentOS/7 is at location: /home/username/.apptainer/images/CentOS-7_20230116143612.sif

Tip

After the module is loaded for the first time, the prepared image is copied into your home folder to the .apptainer/images subfolder.

Wrappers

image-exec

Executes the given command inside the Apptainer image. The container is in this case started, then the command is executed and the container is stopped.

$ ml CentOS/7
$ image-exec cat /etc/redhat-release
CentOS Linux release 7.9.2009 (Core)

image-mpi

MPI wrapper - see more in the Examples MPI section.

image-run

This command runs the runscript inside the Apptainer image. Note, that the prepared images do not contain a runscript.

image-shell

Invokes an interactive shell inside the Apptainer image.

$ ml CentOS/7
$ image-shell
Apptainer>

Update Image

This command is for updating your local Apptainer image copy. The local copy is overridden in this case.

$ ml CentOS/7
New version of CentOS image was found. (New: CentOS-7_20230116143612.sif Old: CentOS-7_20230115143612.sif)
For updating image use: image-update
Your image of CentOS/7 is at location: /home/username/.apptainer/images/CentOS-7_20230115143612.sif
$ image-update
New version of CentOS image was found. (New: CentOS-7_20230116143612.sif Old: CentOS-7_20230115143612.sif)
Do you want to update local copy? (WARNING all user modification will be deleted) [y/N]: y
Updating image  CentOS-7_20230116143612.sif
       2.71G 100%  199.49MB/s    0:00:12 (xfer#1, to-check=0/1)

sent 2.71G bytes  received 31 bytes  163.98M bytes/sec
total size is 2.71G  speedup is 1.00
New version is ready. (/home/username/.apptainer/images/CentOS-7_20230116143612.sif)

MPI

In the following example, we are using a job submitted by the command: qsub -A PROJECT -q qprod -l select=2:mpiprocs=128 -l walltime=00:30:00 -I

Note

We have seen no major performance impact for a job running in a Apptainer container.

With Apptainer, the MPI usage model is to call mpirun from outside the container and reference the container from your mpirun command. Usage would look like this:

$ mpirun -np 128 apptainer exec container.img /path/to/contained_mpi_prog

By calling mpirun outside of the container, we solve several very complicated work-flow aspects. For example, if mpirun is called from within the container, it must have a method for spawning processes on remote nodes. Historically the SSH is used for this, which means that there must be an sshd running within the container on the remote nodes and this sshd process must not conflict with the sshd running on that host. It is also possible for the resource manager to launch the job and (in OpenMPI’s case) the Orted (Open RTE User-Level Daemon) processes on the remote system, but that then requires resource manager modification and container awareness.

In the end, we do not gain anything by calling mpirun from within the container except for increasing the complexity levels and possibly losing out on some added performance benefits (e.g. if a container was not built with the proper OFED as the host).

MPI Inside Apptainer Image

$ ml CentOS/7
$ image-shell
Apptainer> mpirun hostname | wc -l
128

As you can see in this example, we allocated two nodes, but MPI can use only one node (128 processes) when used inside the Apptainer image.

MPI Outside Apptainer Image

$ ml CentOS/7
Your image of CentOS/7 is at location: /home/username/.apptainer/images/CentOS-7_20230116143612.sif
$ image-mpi hostname | wc -l
256

In this case, the MPI wrapper behaves like the mpirun command. The mpirun command is called outside the container and the communication between nodes are propagated into the container automatically.

How to Use Own Image on Cluster?

  • Prepare the image on your computer
  • Transfer the images to your /home directory on the cluster (for example .apptainer/image)
local:$ scp container.img login@login2.clustername.it4i.cz:~/.apptainer/image/container.img
  • Load module Apptainer (ml apptainer)
  • Use your image

Note

If you want to use the Apptainer wrappers with your own images, load the apptainer-wrappers/1.0 module and set the environment variable IMAGE_PATH_LOCAL=/path/to/container.img.

How to Edit IT4Innovations Image?

  • Transfer the image to your computer
local:$ scp login@login2.clustername.it4i.cz:/home/username/.apptainer/image/container.img container.img
  • Modify the image
  • Transfer the image from your computer to your /home directory on the cluster
local:$ scp container.img login@login2.clustername.it4i.cz:/home/username/.apptainer/image/container.img
  • Load module Apptainer (ml apptainer)
  • Use your image

Comments