Singularity

Modified

September 16, 2024

Requirements

Building SIF images

The equivalent to a Dockerfile for singularity is Singularity definition file where the instructions for the image are specified.

Bootstrap: docker
From: debian:stable
Stage: build

%post
    apt-get update && apt-get install -y jupyter-notebook python3-matplotlib python3-pandas python3-numpy
%labels
    Author Name Surname <abc123@ku.dk>
    Version v1.0
# Build the image
singularity build --fakeroot  <my-app>.sif <my-app>.def
# Run the container 
singularity run <my-app>.sif jupyter-notebook
Tips

Limitations

  • Keep in mind that Singularity always operates using your user ID, meaning you cannot switch to the root user inside a Singularity container. This will cause troubles when installing package managers like apt.
  • SIF images are not writable by default.

Solution

  • --fakeroot option is used to create a container image with root-like permissions without requiring actual root access on the host system. This is particularly useful for users who need to build or modify containers (installing software) in environments where they do not have superuser privileges.

Using Docker images

Let’s use the same docker image as in the Docker section.

singularity pull docker://debian@sha256:2171c87301e5ea528cee5c2308a4589f8f2ac819d4d434b679b7cb1dc8de6912

# creates a sif 
singularity shell debian@sha256_2171c87301e5ea528cee5c2308a4589f8f2ac819d4d434b679b7cb1dc8de6912.sif

# Let's check a couple commands on the host machine  (as we did in the previous module)

gzip --version # same as docker
hostname # vagrant (macß) different
whoami # vagrant (docker is root)

# deploy the container  
singularity shell debian@sha256_2171c87301e5ea528cee5c2308a4589f8f2ac819d4d434b679b7cb1dc8de6912.sif

# Install filter in the container 
apt-get install filter

# Alternative command to install filter
singularity exec docker://debian@sha256:2171c87301e5ea528cee5c2308a4589f8f2ac819d4d434b679b7cb1dc8de6912 bash -c "apt install filter 2>&1 || true "
Tip

The docker tag (docker://) step is required as singularity has sometimes trouble handling the sha256, image description.

Other important information to consider:

  • Singularity Hub is no longer maintained. Alternatives: git-annex for hosting images.
  • SIF images are much smaller than Docker images.