Skip to content

Latest commit

 

History

History
119 lines (84 loc) · 5.43 KB

singularity.md

File metadata and controls

119 lines (84 loc) · 5.43 KB
description
Singularity container platform

Singularity

# Get a singularity image and run (runscript)
$ singularity pull hello-world.sif shub://vsoch/hello-world
$ singularity run hello-world.sif

# Inspect run-script
$ singularity inspect -r hello-world.sif

# View singularity cache (where deleted images stored)
$ singularity cache list
$ singularity cache list -v

# Clean the cache 
$ singularity cache clean

# Run specific command within a container
$ singularity exec hello-world.sif /bin/echo Hello World!

# Open an interactive shell within a container
$ singularity shell hello-world.sif 
Singularity>

Singularity binds some directories from the host system into the running container. By default, one directory is home, another is the current working directory where you started singularity command. 

Host system:                                                      Singularity container:
-------------                                                     ----------------------
/                                                                 /
├── bin                                                           ├── bin
├── etc                                                           ├── etc
│   ├── ...                                                       │   ├── ...
│   ├── group  ─> user's group added to group file in container ─>│   ├── group
│   └── passwd ──> user info added to passwd file in container ──>│   └── passwd
├── home                                                          ├── usr
│   └── jc1000 ───> user home directory made available ──> ─┐     ├── sbin
├── usr                 in container via bind mount         │     ├── home
├── sbin                                                    └────────>└── jc1000
└── ...                                                           └── ...

You can specify addtional host system directories to be available in the container by -B

# Bind additional host system directories to the container
$ singularity shell -B /work/z19/shared hello-world.sif
Singularity> ls /work/z19/shared

# Specify where a host directory is mounted in the container with :
$ singularity shell -B /work/z19/shared:/shared-data hello-world.sif
Singularity> ls /shared-data

Singularity can pull docker images from docker hub. Singularity pulls the slices or layers that make up the Docker image and converts them into a single-file Singularity SIF image.

$ singularity pull python-3.9.6.sif docker://python:3.9.6-slim-buster
$ singularity run python-3.9.6.sif

--fakeroot allows sudo command for non-root users to package (tar, zip) files and build images.

Build Singularity images (.sif) with Singularity Definition File (.def)

# Where to bootstrap image from
Bootstrap: docker
From: ubuntu:20.04

# Shell commands run in images context
%post
    apt-get -y update && \
    apt-get install -y python3

# Define the runscript
%runscript
    python3 -c 'print("Hello World! Hello from our custom Singularity image!")'
$ singularity build /home/test_image.sif /home/test_image.def

For more definition file writings:
https://docs.sylabs.io/guides/3.5/user-guide/definition_files.html#sections

Use scp (secure copy) to copy files between systems

You may find that the created Singularity image file on your host filesystem is owned by the root user and not your user. In this case, you won’t be able to change the ownership/permissions of the file directly if you don’t have root access.

However, the image file will be readable by you and you should be able to take a copy of the file under a new name which you will then own. You will then be able to modify the permissions of this copy of the image and delete the original root-owned file since the default permissions should allow this.

It is recommended that you move the created .sif file to a platform with an installation of Singularity, rather than attempting to run the image using the Docker container.

$ scp -i /path/to/keyfile/id_mykey ./my_image.sif xli07@ntu.nscc.sg:/home/xli072

Additional Singularity features

  • Remote Builder Capabilities: If you have access to a platform with Singularity installed but you don’t have root access to create containers, you may be able to use the Remote Builder functionality to offload the process of building an image to remote cloud resources. You’ll need to register for a cloud token via the link on the Remote Builder page.
  • Signing containers: Singularity supports signing containers. This allows a digital signature to be linked to an image file. This signature can be used to verify that an image file has been signed by the holder of a specific key and that the file is unchanged from when it was signed. You can find full details of how to use this functionality in the Singularity documentation on Signing and Verifying Containers.

Running MPI with Singularity

References

{% embed url="https://singularity-tutorial.github.io/01-installation/" %}

{% embed url="https://epcced.github.io/2021-07-29_Singularity_Online/" %}