For more information see: https://www.sylabs.io/docs/
The basic idea behind Singularity containers is that software is packaged into a container (basically an entire self-contained operating system!) that is based on a Docker image that can then be run by the user. This allows hard to install software to be easily packaged and used - because you are packaging the entire OS!
During runtime, the root file system
/ is changed to the one inside the
image and file systems are brought into the container through bind
mounts. This sounds complicated, but in practice this is easy due to
singularity_wrapper written for Triton.
While the image itself is read-only, remember that
/l etc. are not. If you edit/remove files in these locations within
the image, that will happen outside the image as well.
On Triton, you just need to load the proper module. This will set
some environment variables and enable the use of
singularity_wrapper is written so that when you load a module written
for a singularity image, all the important options are already handled
for you. It has three basic commands:
singularity_wrapper shell <shell>- Gives user a shell within the image (specify
<shell>to say which shell you want).
singularity_wrapper exec <cmd>- Executes a program within the image.
singularity_wrapper run <parameters>- Runs the singularity image. What this means depends on the image in question - each image will define a “run command” which does something. If you don’t know what this is, use the first two instead.
Under the hood,
singularity_wrapper does this:
- Choosing appropriate image based on module version
- Binding of basic paths (
- Loading of system libraries within images (if needed) (e.g.
- Setting working directory within image (if needed)
These are the “raw” singularity commands. If you use these, you have
to configure the images and bind mounts yourself (which is done
singularity_wrapper). If you
module show the
module you can get hints about what happens.
Singularity enables three base commands to user:
singularity shell <image>- Gives user a shell within the image (see
singularity shell --helpfor more information on flags etc.)
singularity exec <image> <cmd>- Executes a program within the image (see
singularity exec --helpfor more information on flags etc.)
singularity run <image> <parameters>- Runs the singularity image. What this means depends on the image in question. (see
singularity run --helpfor more information on flags etc.)
Creating your own Singularity images to run in Triton¶
All images used in Triton are built from Docker images stored in our private Docker registry in registry.cs.aalto.fi. They build automatically from Docker pushes using our continuous integration builder. If you want to build your own Singularity image to Triton, we can create a user for you to the registry and add your image to the automatic build.
Even though the system is in production it is still being tested. Thus there might be changes in the future.
Steps to get your images building are outlined below. You’ll need to do steps 1 to 3 only once.
Step 1: Log in to registry.cs.aalto.fi¶
registry.cs.aalto.fi and click
Social logins. This will redirect you to a
Gitlab-page that you can use
for authentication. In this page use your Aalto username and password to login.
In the future we’ll improve the authentication page.
Step 2: Create an application token¶
For added security you cannot use your main password for
By clicking on your username, you’ll get to your user settings. From there, do
Create new tokenin the Application tokens-section.
- Choose name for the token and click create.
- Copy the application token that is visible on the right side of your screen.
Step 3: Docker login¶
On your own workstation run:
docker login registry.cs.aalto.fi
Your username is same as your Aalto username. As a password give the application token you created in step 2.
Step 4: Push your images to registry¶
If you have an existing image in Dockerhub, you can run:
docker pull <dockerhub user>/<image>:<tag> docker tag <dockerhub user>/<image>:<tag> registry.cs.aalto.fi/<your username>/<image>:<tag> docker push registry.cs.aalto.fi/<your username>/<image>:<tag>
docker pull library/ubuntu:latest docker tag library/ubuntu:latest registry.cs.aalto.fi/$USER/ubuntu:latest docker push registry.cs.aalto.fi/$USER/ubuntu:latest
If you are building your image from Dockerfile, you can run:
docker build -it registry.cs.aalto.fi/$USER/my_image:latest /path/to/my/dockerfile docker push registry.cs.aalto.fi/$USER/my_image:latest
Step 5: Let us know what image you want to have in Triton¶
Do note that images built to Triton are visible to all users. Do not include sensitive code/data in the docker images. You should retreive such data from your project/work folder during job runtime.
We need the following information for the automatic build:
- What is the Docker url of the image (e.g.
- What tags do you want built (we recommend you use
- Does the image utilize GPUs?
After that we’ll set up the automated build. Every time you push a newer
version of said
image:tag the image will update in Triton if the build
After the build has been done you can load up your new image in Triton with:
module use /share/apps/singularity-ci/centos/modules/$USER module load my_image:latest
and launch the programs within using the