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Singularity
Maneesh Sutar
2023-06-06
2024-10-05
Singularity Container Engine

Singularity Container Engine

Pull

Docker images are stored in layers, so pull must also combine those layers into a usable SingularityCE file (.SIF file).

To pull image from dockerhub:

singularity pull docker://<path>

To pull from container library (Sylabs)

singularity pull library://<path>

pull command creates a new .sif file in the current directory.

Build

To create images from other images or from scratch using a definition file
Also to convert an image between the container formats

e.g. Following commands downloads pre-build images from external sources and converts them to .sif format

singularity build <IMAGE_PATH> docker://<path>

Definition Files

Doc

Equivalent to Dockerfiles. Standard extension is .def.

Comparision with Dockerfile

A SingularityCE Definition file is divided into two parts:

  1. Header: describes the core operating system to build within the container. Similar to FROM in Dockerfile.

  2. Sections: Similar to layers in Dockerfile. Each section in SIF file is defined by a % character followed by the name of the particular section.

Shell, Exec, Run, Instance Start

The shell command allows you to spawn a new shell within your container and interact with it as though it were a virtual machine.Once inside of a SingularityCE container, you are the same user as you are on the host system
Equivalen to singularity exec <image file path> sh

The exec command allows you to execute a custom command within a container by specifying the image file.
To exec, a command to run MUST be passed.

The run command is same as docker, which will run the container using given image. This is equivalent to ./sif-file-path. This calls %runscript block from the defination file.
Use run --containall  to run a SingularityCE image in an isolated manner:

The instance start command allows you to create a new named instance from an existing container image that will begin running in the background. Name must be passed as argument after image file path. This calls %startscript block from the defination file
To see list of running containers, singularity instance list
To stop container, singularity instance stop <name of container>

By default, Singularity mounts /home directory to the container.
To disable, run with --no-home
To clear env variables, run with --cleanenv

Bind and Mount Directories

Just like Docker, --bind and --mount commands can be used to mount directories.
 By default, SingularityCE bind mounts /home/$USER, /tmp, and $PWD into your container at runtime.

References

  1. https://docs.sylabs.io/guides/latest/user-guide/
  2. https://biohpc.cornell.edu/doc/singularity_v3.pdf