Quick Start

This guide is intended for running Singularity on a computer where you have root (administrative) privileges, and will install Singularity from source code. Other installation options, including building an RPM package and installing Singularity without root privileges are discussed in the installation section of the admin guide.

If you need to request an installation on your shared resource, see the requesting an installation section for information to send to your system administrator.

For any additional help or support contact the Singularity Community: https://singularity.hpcng.org/help

Quick Installation Steps

You will need a Linux system to run Singularity natively. Options for using Singularity on Mac and Windows machines, along with alternate Linux installation options are discussed in the installation section of the admin guide.

Install system dependencies

You must first install development libraries to your host. Assuming Ubuntu (apply similar to RHEL derivatives):

$ sudo apt-get update && sudo apt-get install -y \
    build-essential \
    libssl-dev \
    uuid-dev \
    libgpgme11-dev \
    squashfs-tools \
    libseccomp-dev \
    wget \
    pkg-config \
    git \
    cryptsetup

Note

Note that squashfs-tools is only a dependency for commands that build images. The build command obviously relies on squashfs-tools, but other commands may do so as well if they are ran using container images from Docker Hub for instance.

There are 3 broad steps to installing Singularity:

  1. Installing Go

  2. Downloading Singularity

  3. Compiling Singularity Source Code

Install Go

Singularity v3 and above is written primarily in Go, so you will need Go installed to compile it from source.

This is one of several ways to install and configure Go.

Note

If you have previously installed Go from a download, rather than an operating system package, you should remove your go directory, e.g. rm -r /usr/local/go before installing a newer version. Extracting a new version of Go over an existing installation can lead to errors when building Go programs, as it may leave old files, which have been removed or replaced in newer versions.

Visit the Go Downloads page and pick a package archive suitable to the environment you are in. Once the Download is complete, extract the archive to /usr/local (or use other instructions on go installation page). Alternatively, follow the commands here:

$ export VERSION=1.14.12 OS=linux ARCH=amd64 && \  # Replace the values as needed
  wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \ # Downloads the required Go package
  sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \ # Extracts the archive
  rm go$VERSION.$OS-$ARCH.tar.gz    # Deletes the ``tar`` file

Set the Environment variable PATH to point to Go:

$ echo 'export PATH=/usr/local/go/bin:$PATH' >> ~/.bashrc && \
  source ~/.bashrc

Download Singularity from a release

You can download Singularity from one of the releases. To see a full list, visit the GitHub release page. After deciding on a release to install, you can run the following commands to proceed with the installation.

$ export VERSION=3.8.0 && # adjust this as necessary \
    wget https://github.com/hpcng/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
    tar -xzf singularity-${VERSION}.tar.gz && \
    cd singularity

Compile the Singularity source code

Now you are ready to build Singularity. Dependencies will be automatically downloaded. You can build Singularity using the following commands:

$ ./mconfig && \
    make -C builddir && \
    sudo make -C builddir install

Singularity must be installed as root to function properly.

Overview of the Singularity Interface

Singularity’s command line interface allows you to build and interact with containers transparently. You can run programs inside a container as if they were running on your host system. You can easily redirect IO, use pipes, pass arguments, and access files, sockets, and ports on the host system from within a container.

The help command gives an overview of Singularity options and subcommands as follows:

$ singularity help

Linux container platform optimized for High Performance Computing (HPC) and
Enterprise Performance Computing (EPC)

Usage:
  singularity [global options...]

Description:
  Singularity containers provide an application virtualization layer enabling
  mobility of compute via both application and environment portability. With
  Singularity one is capable of building a root file system that runs on any
  other Linux system where Singularity is installed.

Options:
  -d, --debug     print debugging information (highest verbosity)
  -h, --help      help for singularity
      --nocolor   print without color output (default False)
  -q, --quiet     suppress normal output
  -s, --silent    only print errors
  -v, --verbose   print additional information

Available Commands:
  build       Build a Singularity image
  cache       Manage the local cache
  capability  Manage Linux capabilities for users and groups
  exec        Run a command within a container
  help        Help about any command
  inspect     Show metadata for an image
  instance    Manage containers running as services
  key         Manage OpenPGP keys
  oci         Manage OCI containers
  plugin      Manage singularity plugins
  pull        Pull an image from a URI
  push        Upload image to the provided library (default is "cloud.sylabs.io")
  remote      Manage singularity remote endpoints
  run         Run the user-defined default command within a container
  run-help    Show the user-defined help for an image
  search      Search a Container Library for images
  shell       Run a shell within a container
  sif         siftool is a program for Singularity Image Format (SIF) file manipulation
  sign        Attach a cryptographic signature to an image
  test        Run the user-defined tests within a container
  verify      Verify cryptographic signatures attached to an image
  version     Show the version for Singularity

Examples:
  $ singularity help <command> [<subcommand>]
  $ singularity help build
  $ singularity help instance start


For additional help or support, please visit https://www.sylabs.io/docs/

Information about subcommand can also be viewed with the help command.

$ singularity help verify
Verify cryptographic signatures attached to an image

Usage:
  singularity verify [verify options...] <image path>

Description:
  The verify command allows a user to verify cryptographic signatures on SIF
  container files. There may be multiple signatures for data objects and
  multiple data objects signed. By default the command searches for the primary
  partition signature. If found, a list of all verification blocks applied on
  the primary partition is gathered so that data integrity (hashing) and
  signature verification is done for all those blocks.

Options:
  -a, --all               verify all objects
  -g, --group-id uint32   verify objects with the specified group ID
  -h, --help              help for verify
  -j, --json              output json
      --legacy-insecure   enable verification of (insecure) legacy signatures
  -l, --local             only verify with local keys
  -i, --sif-id uint32     verify object with the specified ID
  -u, --url string        key server URL (default "https://keys.sylabs.io")


Examples:
  $ singularity verify container.sif


For additional help or support, please visit https://www.sylabs.io/docs/

Singularity uses positional syntax (i.e. the order of commands and options matters). Global options affecting the behavior of all commands follow the main singularity command. Then sub commands are followed by their options and arguments.

For example, to pass the --debug option to the main singularity command and run Singularity with debugging messages on:

$ singularity --debug run library://sylabsed/examples/lolcow

To pass the --containall option to the run command and run a Singularity image in an isolated manner:

$ singularity run --containall library://sylabsed/examples/lolcow

Singularity 2.4 introduced the concept of command groups. For instance, to list Linux capabilities for a particular user, you would use the list command in the capability command group like so:

$ singularity capability list dave

Container authors might also write help docs specific to a container or for an internal module called an app. If those help docs exist for a particular container, you can view them like so.

$ singularity inspect --helpfile container.sif  # See the container's help, if provided

$ singularity inspect --helpfile --app=foo foo.sif  # See the help for foo, if provided

Download pre-built images

You can use the search command to locate groups, collections, and containers of interest on the Container Library .

singularity search tensorflow
Found 22 container images for amd64 matching "tensorflow":

    library://ajgreen/default/tensorflow2-gpu-py3-r-jupyter:latest
            Current software: tensorflow2; py3.7; r; jupyterlab1.2.6
            Signed by: 1B8565093D80FA393BC2BD73EA4711C01D881FCB

    library://bensonyang/collection/tensorflow-rdma_v4.sif:latest

    library://dxtr/default/hpc-tensorflow:0.1

    library://emmeff/tensorflow/tensorflow:latest

    library://husi253/default/tensorflow:20.01-tf1-py3-mrcnn-2020.10.07

    library://husi253/default/tensorflow:20.01-tf1-py3-mrcnn-20201014

    library://husi253/default/tensorflow:20.01-tf2-py3-lhx-20201007

    library://irinaespejo/default/tensorflow-gan:sha256.0c1b6026ba2d6989242f418835d76cd02fc4cfc8115682986395a71ef015af18

    library://jon/default/tensorflow:1.12-gpu
            Signed by: D0E30822F7F4B229B1454388597B8AFA69C8EE9F

    ...

You can use the pull and build commands to download pre-built images from an external resource like the Container Library or Docker Hub.

When called on a native Singularity image like those provided on the Container Library, pull simply downloads the image file to your system.

$ singularity pull library://lolcow

You can also use pull with the docker:// uri to reference Docker images served from a registry. In this case pull does not just download an image file. Docker images are stored in layers, so pull must also combine those layers into a usable Singularity file.

$ singularity pull docker://godlovedc/lolcow

Pulling Docker images reduces reproducibility. If you were to pull a Docker image today and then wait six months and pull again, you are not guaranteed to get the same image. If any of the source layers has changed the image will be altered. If reproducibility is a priority for you, try building your images from the Container Library.

You can also use the build command to download pre-built images from an external resource. When using build you must specify a name for your container like so:

$ singularity build ubuntu.sif library://ubuntu

$ singularity build lolcow.sif docker://godlovedc/lolcow

Unlike pull, build will convert your image to the latest Singularity image format after downloading it. build is like a “Swiss Army knife” for container creation. In addition to downloading images, you can use build to create images from other images or from scratch using a definition file. You can also use build to convert an image between the container formats supported by Singularity. To see a comparison of Singularity definition file with Dockerfile, please see: this section.

Interact with images

You can interact with images in several ways, each of which can accept image URIs in addition to a local image path.

For demonstration, we will use a lolcow_latest.sif image that can be pulled from the Container Library:

$ singularity pull library://sylabsed/examples/lolcow

Shell

The shell command allows you to spawn a new shell within your container and interact with it as though it were a small virtual machine.

$ singularity shell lolcow_latest.sif

Singularity lolcow_latest.sif:~>

The change in prompt indicates that you have entered the container (though you should not rely on that to determine whether you are in container or not).

Once inside of a Singularity container, you are the same user as you are on the host system.

Singularity lolcow_latest.sif:~> whoami
david

Singularity lolcow_latest.sif:~> id
uid=1000(david) gid=1000(david) groups=1000(david),4(adm),24(cdrom),27(sudo),30(dip),46(plugdev),116(lpadmin),126(sambashare)

shell also works with the library://, docker://, and shub:// URIs. This creates an ephemeral container that disappears when the shell is exited.

$ singularity shell library://sylabsed/examples/lolcow

Executing Commands

The exec command allows you to execute a custom command within a container by specifying the image file. For instance, to execute the cowsay program within the lolcow_latest.sif container:

$ singularity exec lolcow_latest.sif cowsay moo
 _____
< moo >
 -----
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

exec also works with the library://, docker://, and shub:// URIs. This creates an ephemeral container that executes a command and disappears.

$ singularity exec library://sylabsed/examples/lolcow cowsay "Fresh from the library!"
 _________________________
< Fresh from the library! >
 -------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Running a container

Singularity containers contain runscripts. These are user defined scripts that define the actions a container should perform when someone runs it. The runscript can be triggered with the run command, or simply by calling the container as though it were an executable.

$ singularity run lolcow_latest.sif
 _____________________________________
/ You have been selected for a secret \
\ mission.                            /
 -------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

$ ./lolcow_latest.sif
 ____________________________________
/ Q: What is orange and goes "click, \
\ click?" A: A ball point carrot.    /
 ------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

run also works with the library://, docker://, and shub:// URIs. This creates an ephemeral container that runs and then disappears.

$ singularity run library://sylabsed/examples/lolcow
 ____________________________________
/ Is that really YOU that is reading \
\ this?                              /
 ------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Working with Files

Files on the host are reachable from within the container.

$ echo "Hello from inside the container" > $HOME/hostfile.txt

$ singularity exec lolcow_latest.sif cat $HOME/hostfile.txt

Hello from inside the container

This example works because hostfile.txt exists in the user’s home directory. By default Singularity bind mounts /home/$USER, /tmp, and $PWD into your container at runtime.

You can specify additional directories to bind mount into your container with the --bind option. In this example, the data directory on the host system is bind mounted to the /mnt directory inside the container.

$ echo "Drink milk (and never eat hamburgers)." > /data/cow_advice.txt

$ singularity exec --bind /data:/mnt lolcow_latest.sif cat /mnt/cow_advice.txt
Drink milk (and never eat hamburgers).

Pipes and redirects also work with Singularity commands just like they do with normal Linux commands.

$ cat /data/cow_advice.txt | singularity exec lolcow_latest.sif cowsay
 ________________________________________
< Drink milk (and never eat hamburgers). >
 ----------------------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Build images from scratch

Singularity v3.0 and above produces immutable images in the Singularity Image File (SIF) format. This ensures reproducible and verifiable images and allows for many extra benefits such as the ability to sign and verify your containers.

However, during testing and debugging you may want an image format that is writable. This way you can shell into the image and install software and dependencies until you are satisfied that your container will fulfill your needs. For these scenarios, Singularity also supports the sandbox format (which is really just a directory).

Sandbox Directories

To build into a sandbox (container in a directory) use the build --sandbox command and option:

$ sudo singularity build --sandbox ubuntu/ library://ubuntu

This command creates a directory called ubuntu/ with an entire Ubuntu Operating System and some Singularity metadata in your current working directory.

You can use commands like shell, exec , and run with this directory just as you would with a Singularity image. If you pass the --writable option when you use your container you can also write files within the sandbox directory (provided you have the permissions to do so).

$ sudo singularity exec --writable ubuntu touch /foo

$ singularity exec ubuntu/ ls /foo
/foo

Converting images from one format to another

The build command allows you to build a container from an existing container. This means that you can use it to convert a container from one format to another. For instance, if you have already created a sandbox (directory) and want to convert it to the default immutable image format (squashfs) you can do so:

$ singularity build new-sif sandbox

Doing so may break reproducibility if you have altered your sandbox outside of the context of a definition file, so you are advised to exercise care.

Singularity Definition Files

For a reproducible, verifiable and production-quality container you should build a SIF file using a Singularity definition file. This also makes it easy to add files, environment variables, and install custom software, and still start from your base of choice (e.g., the Container Library).

A definition file has a header and a body. The header determines the base container to begin with, and the body is further divided into sections that perform things like software installation, environment setup, and copying files into the container from host system, etc.

Here is an example of a definition file:

BootStrap: library
From: ubuntu:16.04

%post
    apt-get -y update
    apt-get -y install fortune cowsay lolcat

%environment
    export LC_ALL=C
    export PATH=/usr/games:$PATH

%runscript
    fortune | cowsay | lolcat

%labels
    Author GodloveD

To build a container from this definition file (assuming it is a file named lolcow.def), you would call build like so:

$ sudo singularity build lolcow.sif lolcow.def

In this example, the header tells Singularity to use a base Ubuntu 16.04 image from the Container Library.

  • The %post section executes within the container at build time after the base OS has been installed. The %post section is therefore the place to perform installations of new applications.

  • The %environment section defines some environment variables that will be available to the container at runtime.

  • The %runscript section defines actions for the container to take when it is executed.

  • And finally, the %labels section allows for custom metadata to be added to the container.

This is a very small example of the things that you can do with a definition file. In addition to building a container from the Container Library, you can start with base images from Docker Hub and use images directly from official repositories such as Ubuntu, Debian, CentOS, Arch, and BusyBox. You can also use an existing container on your host system as a base.

If you want to build Singularity images but you don’t have administrative (root) access on your build system, you can build images using the Remote Builder.

This quickstart document just scratches the surface of all of the things you can do with Singularity!

If you need additional help or support, see https://singularity.hpcng.org/help.

Singularity on a shared resource

Perhaps you are a user who wants a few talking points and background to share with your administrator. Or maybe you are an administrator who needs to decide whether to install Singularity.

This document, and the accompanying administrator documentation provides answers to many common questions.

If you need to request an installation you may decide to draft a message similar to this:

Dear shared resource administrator,

We are interested in having Singularity (https://singularity.hpcng.org)
installed on our shared resource. Singularity containers will allow us to
build encapsulated environments, meaning that our work is reproducible and
we are empowered to choose all dependencies including libraries, operating
system, and custom software. Singularity is already in use on many of the
top HPC centers around the world. Examples include:

    Texas Advanced Computing Center
    GSI Helmholtz Center for Heavy Ion Research
    Oak Ridge Leadership Computing Facility
    Purdue University
    National Institutes of Health HPC
    UFIT Research Computing at the University of Florida
    San Diego Supercomputing Center
    Lawrence Berkeley National Laboratory
    University of Chicago
    McGill HPC Centre/Calcul Québec
    Barcelona Supercomputing Center
    Sandia National Lab
    Argonne National Lab

Importantly, it has a vibrant team of developers, scientists, and HPC
administrators that invest heavily in the security and development of the
software, and are quick to respond to the needs of the community. To help
learn more about Singularity, I thought these items might be of interest:

    - Security: A discussion of security concerns is discussed at
    https://singularity.hpcng.org/admin-docs/3.8/admin_quickstart.html

    - Installation:
    https://singularity.hpcng.org/admin-docs/3.8/installation.html

If you have questions about any of the above, you can contact one
of the sources listed at https://singularity.hpcng.org/help.  I can
do my best to facilitate this interaction if help is needed.

Thank you kindly for considering this request!

Best,

User