Singularity Container Ation User Guide 3.0
User Manual:
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Page Count: 26
- Quick Start
- Signing and Verifying Containers
- Build a Container
- Security Options
Singularity Container Documentation
Release 3.0
User Docs
Oct 13, 2018
CONTENTS
1 Quick Start 1
1.1 Quick Installation Steps ......................................... 1
1.1.1 Install system dependencies .................................. 1
1.1.2 Install Go ............................................ 1
1.1.3 Clone the Singularity repository ................................ 2
1.1.4 Install Go dependencies ..................................... 2
1.1.5 Compile the Singularity binary ................................. 2
1.2 Overview of the Singularity Interface .................................. 2
1.3 Download pre-built images ........................................ 4
1.4 Interact with images ........................................... 5
1.4.1 Shell ............................................... 5
1.4.2 Executing Commands ...................................... 6
1.4.3 Running a container ....................................... 6
1.4.4 Working with Files ....................................... 7
1.5 Build images from scratch ........................................ 8
1.5.1 Sandbox Directories ...................................... 8
1.5.2 Converting images from one format to another ......................... 8
1.5.3 Singularity Definition Files ................................... 9
2 Signing and Verifying Containers 11
2.1 Verifying containers from the Container Library ............................ 11
2.2 Signing your own containers ....................................... 11
2.2.1 Generating and managing PGP keys .............................. 11
2.2.2 Signing and validating your own containers .......................... 12
3 Build a Container 15
3.1 Overview ................................................. 15
3.2 Downloading an existing container from the Container Library ..................... 15
3.3 Downloading an existing container from Docker Hub .......................... 16
3.4 Creating writable --sandbox directories ............................... 16
3.5 Converting containers from one format to another ............................ 16
3.6 Building containers from Singularity definition files .......................... 16
3.7 Build options ............................................... 17
3.7.1 --builder .......................................... 17
3.7.2 --detached ......................................... 17
3.7.3 --force ............................................ 17
3.7.4 --json ............................................. 17
3.7.5 --library .......................................... 17
3.7.6 --notest ........................................... 17
3.7.7 --remote ........................................... 17
i
3.7.8 --sandbox .......................................... 18
3.7.9 --section .......................................... 18
3.7.10 --update ........................................... 18
3.8 More Build topics ............................................ 18
4 Security Options 19
4.1 Linux Capabilities ............................................ 19
4.2 Security related action options ...................................... 20
4.2.1 --add-caps ......................................... 20
4.2.2 --allow-setuid ...................................... 20
4.2.3 --keep-privs ........................................ 20
4.2.4 --drop-caps ......................................... 20
4.2.5 --security ......................................... 21
ii
CHAPTER
ONE
QUICK START
This guide is intended for running Singularity on a computer where you have root (administrative) privileges.
If you need to request an installation on your shared resource, see the requesting an installation help page for informa-
tion to send to your system administrator.
For any additional help or support contact the Sylabs team: https://www.sylabs.io/contact/
1.1 Quick Installation Steps
You will need a Linux system to run Singularity.
See the installation page for information about installing older versions of Singularity.
1.1.1 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
1.1.2 Install Go
Singularity 3.0 is written primarily in Go, and you will need Go installed to compile it from source.
This is one of several ways to install and configure Go.
First, visit the Go download page and pick the appropriate Go archive (>=1.11.1). Copy the link address and download
with wget like so:
$ export VERSION=1.11 OS=linux ARCH=amd64
$ cd /tmp
$ wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz
Then extract the archive to /usr/local
$ sudo tar -C /usr/local -xzf go$VERSION.$OS-$ARCH.tar.gz
Finally, set up your environment for Go
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$ echo 'export GOPATH=${HOME}/go' >> ~/.bashrc
$ echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc
$ source ~/.bashrc
1.1.3 Clone the Singularity repository
Go is a bit finicky about where things are placed. Here is the correct way to build Singularity from source.
$ mkdir -p $GOPATH/src/github.com/sylabs
$ cd $GOPATH/src/github.com/sylabs
$ git clone https://github.com/sylabs/singularity.git
$ cd singularity
1.1.4 Install Go dependencies
Dependencies are managed using Dep. You can use go get to install it like so:
$ go get -u -v github.com/golang/dep/cmd/dep
1.1.5 Compile the Singularity binary
Now you are ready to build Singularity. Dependencies will be automatically downloaded. You can build Singularity
using the following commands:
$ cd $GOPATH/src/github.com/sylabs/singularity
$ ./mconfig
$ make -C builddir
$ sudo make -C builddir install
Singularity must be installed as root to function properly.
1.2 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
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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
-q, --quiet suppress normal output
-s, --silent only print errors
-t, --tokenfile string path to the file holding your sylabs
authentication token (default
"/home/david/.singularity/sylabs-token")
-v, --verbose print additional information
Available Commands:
build Build a new Singularity container
capability Manage Linux capabilities on containers
exec Execute a command within container
help Help about any command
inspect Display metadata for container if available
instance Manage containers running in the background
keys Manage OpenPGP key stores
pull Pull a container from a URI
push Push a container to a Library URI
run Launch a runscript within container
run-help Display help for container if available
search Search the library
shell Run a Bourne shell within container
sign Attach cryptographic signatures to container
test Run defined tests for this particular container
verify Verify cryptographic signatures on container
version Show application version
Examples:
$ singularity help <command>
Additional help for any Singularity subcommand can be seen by appending
the subcommand name to the above command.
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 on container
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:
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-g, --groupid uint32 group ID to be verified
-h, --help help for verify
-i, --id uint32 descriptor ID to be verified
-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 com-
mands are passed 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 capabilities command group like so:
$ singularity capability list --user 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 help container.sif # See the container's help, if provided
$ singularity help --app foo container.sif # See the help for foo, if provided
1.3 Download pre-built images
You can use the search command to locate groups, collections, and containers of interest on the Container Library .
$ singularity search alp
No users found for 'alp'
Found 1 collections for 'alp'
library://jchavez/alpine
Found 5 containers for 'alp'
library://jialipassion/official/alpine
Tags: latest
library://dtrudg/linux/alpine
Tags: 3.2 3.3 3.4 3.5 3.6 3.7 3.8 edge latest
library://sylabsed/linux/alpine
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Tags: 3.6 3.7 latest
library://library/default/alpine
Tags: 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 latest
library://sylabsed/examples/alpine
Tags: latest
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://sylabsed/linux/alpine
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.
1.4 Interact with images
You can interact with images in several ways. It is not actually necessary to pull or build an image to interact with
it. The commands listed here will work with image URIs in addition to accepting a local path to an image.
For these examples we will use a lolcow_latest.sif image that can be pulled from the Container Library like
so.
$ singularity pull library://sylabsed/examples/lolcow
1.4.1 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.
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$ 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
1.4.2 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 |
|| ||
1.4.3 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.
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$ 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 |
|| ||
1.4.4 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).
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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 |
|| ||
1.5 Build images from scratch
Singularity v3.0 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).
For more details about the different build options and best practices, read about the Singularity flow.
1.5.1 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
1.5.2 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.
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1.5.3 Singularity Definition Files
For a reproducible, 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 do things like install software, setup the environment, and copy files into the container
from the host system.
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, contact the Sylabs team: https://www.sylabs.io/contact/
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CHAPTER
TWO
SIGNING AND VERIFYING CONTAINERS
Singularity 3.0 introduces the abilities to create and manage PGP keys and use them to sign and verify containers. This
provides a trusted method for Singularity users to share containers. It ensures a bit-for-bit reproduction of the original
container as the author intended it.
2.1 Verifying containers from the Container Library
The verify command will allow you to verify that a container has been signed using a PGP key. To use this feature
with images that you pull from the container library, you must first generate an access token to the Sylabs Cloud. If
you don’t already have a valid access token, follow these steps:
1. Go to : https://cloud.sylabs.io/
2. Click “Sign in to Sylabs” and follow the sign in steps.
3. Click on your login id (same and updated button as the Sign in one).
4. Select “Access Tokens” from the drop down menu.
5. Click the “Manage my API tokens” button from the “Account Management” page.
6. Click “Create”.
7. Click “Copy token to Clipboard” from the “New API Token” page.
8. Paste the token string into your ~/.singularity/sylabs-token file.
Now you can verify containers that you pull from the library, ensuring they are bit-for-bit reproductions of the original
image.
$ singularity pull library://alpine
$ singularity verify alpine_latest.sif
Verifying image: alpine_latest.sif
Data integrity checked, authentic and signed by:
Sylabs Admin <support@sylabs.io>, KeyID 51BE5020C508C7E9
In this example you can see that Sylabs Admin has signed the container.
2.2 Signing your own containers
2.2.1 Generating and managing PGP keys
To sign your own containers you first need to generate one or more keys.
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If you attempt to sign a container before you have generated any keys, Singularity will guide you through the interactive
process of creating a new key. Or you can use the newpair subcommand in the key command group like so:.
$ singularity keys newpair
Enter your name (e.g., John Doe) : Dave Godlove
Enter your email address (e.g., john.doe@example.com) : d@sylabs.io
Enter optional comment (e.g., development keys) : demo
Generating Entity and OpenPGP Key Pair... Done
Enter encryption passphrase :
The list subcommand will show you all of the keys you have created or saved locally.‘
$ singularity keys list
Public key listing (/home/david/.singularity/sypgp/pgp-public):
0) U: Dave Godlove (demo) <d@sylabs.io>
C: 2018-10-08 15:25:30 -0400 EDT
F: 135E426D67D8416DE1D6AC7FFED5BBA38EE0DC4A
L: 4096
--------
In the output above, the letters stand for the following:
• U: User
• C: Creation date and time
• F: Fingerprint
• L: Key length
After generating your key you can optionally push it to the Keystore using the fingerprint like so:
$ singularity keys push 135E426D67D8416DE1D6AC7FFED5BBA38EE0DC4A
public key `135E426D67D8416DE1D6AC7FFED5BBA38EE0DC4A` pushed to server successfully
This will allow others to verify images that you have signed.
If you delete your local public PGP key, you can always locate and download it again like so.
$ singularity keys search Godlove
Search results for 'Godlove'
Type bits/keyID Date User ID
--------------------------------------------------------------------------------
pub 4096R/8EE0DC4A 2018-10-08 Dave Godlove (demo) <d@sylabs.io>
--------------------------------------------------------------------------------
$ singularity keys pull 8EE0DC4A
1 key(s) fetched and stored in local cache /home/david/.singularity/sypgp/pgp-public
But note that this only restores the public key (used for verifying) to your local machine and does not restore the
private key (used for signing).
2.2.2 Signing and validating your own containers
Now that you have a key generated, you can use it to sign images like so:
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$ singularity sign my_container.sif
Signing image: my_container.sif
Enter key passphrase:
Signature created and applied to my_container.sif
Because your public PGP key is saved locally you can verify the image without needing to contact the Keystore.
$ singularity verify my_container.sif
Verifying image: my_container.sif
Data integrity checked, authentic and signed by:
Dave Godlove (demo) <d@sylabs.io>, KeyID FED5BBA38EE0DC4A
If you’ve pushed your key to the Keystore you can also verify this image in the absence of a local key. To demonstrate
this, first delete your local keys, and then try to use the verify command again.
$ rm ~/.singularity/sypgp/*
$ singularity verify my_container.sif
Verifying image: my_container.sif
INFO: key missing, searching key server for KeyID: FED5BBA38EE0DC4A...
INFO: key retreived successfully!
Store new public key 135E426D67D8416DE1D6AC7FFED5BBA38EE0DC4A? [Y/n] y
Data integrity checked, authentic and signed by:
Dave Godlove (demo) <d@sylabs.io>, KeyID FED5BBA38EE0DC4A
Answering yes at the interactive prompt will store the Public key locally so you will not have to contact the Keystore
again the next time you verify your container.
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CHAPTER
THREE
BUILD A CONTAINER
build is the “Swiss army knife” of container creation. You can use it to download and assemble existing containers
from external resources like the Container Library and Docker Hub. You can use it to convert containers between
the formats supported by Singularity. And you can use it in conjunction with a Singularity definition file to create a
container from scratch and customized it to fit your needs.
3.1 Overview
The build command accepts a target as input and produces a container as output.
The target defines the method that build uses to create the container. It can be one of the following:
• URI beginning with library:// to build from the Container Library
• URI beginning with docker:// to build from Docker Hub
• URI beginning with shub:// to build from Singularity Hub
• path to a existing container on your local machine
• path to a directory to build from a sandbox
• path to a Singularity definition file
build can produce containers in two different formats that can be specified as follows.
• compressed read-only Singularity Image File (SIF) format suitable for production (default)
• writable (ch)root directory called a sandbox for interactive development ( --sandbox option)
Because build can accept an existing container as a target and create a container in either supported format you can
convert existing containers from one format to another.
3.2 Downloading an existing container from the Container Library
You can use the build command to download a container from the Container Library.
$ sudo singularity build lolcow.simg library://sylabs-jms/testing/lolcow
The first argument (lolcow.simg) specifies a path and name for your container. The second argument
(library://sylabs-jms/testing/lolcow) gives the Container Library URI from which to download. By
default the container will be converted to a compressed, read-only SIF. If you want your container in a writable format
use the --sandbox option.
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3.3 Downloading an existing container from Docker Hub
You can use build to download layers from Docker Hub and assemble them into Singularity containers.
$ sudo singularity build lolcow.sif docker://godlovedc/lolcow
3.4 Creating writable --sandbox directories
If you wanted to create a container within a writable directory (called a sandbox) you can do so with the --sandbox
option. It’s possible to create a sandbox without root privileges, but to ensure proper file permissions it is recommended
to do so as root.
$ sudo singularity build --sandbox lolcow/ library://sylabs-jms/testing/lolcow
The resulting directory operates just like a container in a SIF file. To make changes within the container, use the
--writable flag when you invoke your container. It’s a good idea to do this as root to ensure you have permission
to access the files and directories that you want to change.
$ sudo singularity shell --writable lolcow/
3.5 Converting containers from one format to another
If you already have a container saved locally, you can use it as a target to build a new container. This allows you
convert containers from one format to another. For example if you had a sandbox container called development/
and you wanted to convert it to SIF container called production.sif you could:
$ sudo singularity build production.sif development/
Use care when converting a sandbox directory to the default SIF format. If changes were made to the writable container
before conversion, there is no record of those changes in the Singularity definition file rendering your container non-
reproducible. It is a best practice to build your immutable production containers directly from a Singularity definition
file instead.
3.6 Building containers from Singularity definition files
Of course, Singularity definition files can be used as the target when building a container. For detailed information on
writing Singularity definition files, please see the Container Definition docs. Let’s say you already have the following
container definition file called lolcow.def, and you want to use it to build a SIF container.
Bootstrap: docker
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
(continues on next page)
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(continued from previous page)
%runscript
fortune | cowsay | lolcat
You can do so with the following command.
$ sudo singularity build lolcow.sif lolcow.def
The command requires sudo just as installing software on your local machine requires root privileges.
3.7 Build options
3.7.1 --builder
Singularity 3.0 introduces the option to perform a remote build. The --builder option allows you to specify a URL
to a different build service. For instance, you may need to specify a URL to build to an on premises installation of the
remote builder. This option must be used in conjunction with --remote.
3.7.2 --detached
When used in combination with the --remote option, the --detached option will detach the build from your
terminal and allow it to build in the background without echoing any output to your terminal.
3.7.3 --force
The --force option will delete and overwrite an existing Singularity image without presenting the normal interactive
prompt.
3.7.4 --json
The --json option will force Singularity to interpret a given definition file as a json.
3.7.5 --library
This command allows you to set a different library. (The default library is “https://library.sylabs.io”)
3.7.6 --notest
If you don’t want to run the %test section during the container build, you can skip it with the --notest option.
For instance, maybe you are building a container intended to run in a production environment with GPUs. But perhaps
your local build resource does not have GPUs. You want to include a %test section that runs a short validation but
you don’t want your build to exit with an error because it cannot find a GPU on your system.
3.7.7 --remote
Singularity 3.0 introduces the ability to build a container on an external resource running a remote builder. (The default
remote builder is located at “https://build.sylabs.io”.)
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3.7.8 --sandbox
Build a sandbox (chroot directory) instead of the default SIF format.
3.7.9 --section
Instead of running the entire definition file, only run a specific section or sections. This option accepts a comma
delimited string of definition file sections. Acceptable arguments include all,none or any combination of the
following: setup,post,files,environment,test,labels.
Under normal build conditions, the Singularity definition file is saved into a container’s meta-data so that there is a
record showing how the container was built. Using the --section option may render this meta-data useless, so use
care if you value reproducibility.
3.7.10 --update
You can build into the same sandbox container multiple times (though the results may be unpredictable and it is
generally better to delete your container and start from scratch).
By default if you build into an existing sandbox container, the build command will prompt you to decide whether or
not to overwrite the container. Instead of this behavior you can use the --update option to build _into_ an existing
container. This will cause Singularity to skip the header and build any sections that are in the definition file into the
existing container.
The --update option is only valid when used with sandbox containers.
3.8 More Build topics
• If you want to customize the cache location (where Docker layers are downloaded on your system), specify
Docker credentials, or any custom tweaks to your build environment, see build environment.
• If you want to make internally modular containers, check out the getting started guide here
• If you want to build your containers on the Remote Builder, (because you don’t have root access on a Linux
machine or want to host your container on the cloud) check out this site
18 Chapter 3. Build a Container
CHAPTER
FOUR
SECURITY OPTIONS
Singularity 3.0 introduces many new security related options to the container runtime. This document will describe
the new methods users have for specifying the security scope and context when running Singularity containers.
4.1 Linux Capabilities
Singularity provides full support for granting and revoking Linux capabilities on a user or group basis. For example,
let us suppose that an admin has decided to grant a user capabilities to open raw sockets so that they can use ping in
a container where the binary is controlled via capabilities (i.e. a recent version of CentOS).
To do so, the admin would issue a command such as this:
$ sudo singularity capability add --user david CAP_NET_RAW
This means the user david has just been granted permissions (through Linux capabilities) to open raw sockets within
Singularity containers.
The admin can check that this change is in effect with the capability list command.
$ sudo singularity capability list --user david
CAP_NET_RAW
To take advantage of this new capability, the user david must also request the capability when executing a container
with the --add-caps flag like so:
$ singularity exec --add-caps CAP_NET_RAW library://centos ping -c 1 8.8.8.8
PING 8.8.8.8 (8.8.8.8) 56(84) bytes of data.
64 bytes from 8.8.8.8: icmp_seq=1 ttl=128 time=18.3 ms
--- 8.8.8.8 ping statistics ---
1 packets transmitted, 1 received, 0% packet loss, time 0ms
rtt min/avg/max/mdev = 18.320/18.320/18.320/0.000 ms
If the admin decides that it is no longer necessary to allow the user dave to open raw sockets within Singularity
containers, they can revoke the appropriate Linux capability like so:
$ sudo singularity capability drop --user david CAP_NET_RAW
The capabiltiy add and drop subcommands will also accept the case insensitive keyword all to grant or
revoke all Linux capabilities to a user or group. Similarly, the --add-caps option will accept the all keyword. Of
course appropriate caution should be exercised when using this keyword.
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4.2 Security related action options
Singularity 3.0 introduces many new flags that can be passed to the action commands; shell,exec, and run
allowing fine grained control of security.
4.2.1 --add-caps
As explained above, --add-caps will “activate” Linux capabilities when a container is initiated, providing those
capabilities have been granted to the user by an administrator using the capability add command. This option
will also accept the case insensitive keyword all to add every capability granted by the administrator.
4.2.2 --allow-setuid
The SetUID bit allows a program to be executed as the user that owns the binary. The most well-known SetUID
binaries are owned by root and allow a user to execute a command with elevated privileges. But other SetUID binaries
may allow a user to execute a command as a service account.
By default SetUID is disallowed within Singularity containers as a security precaution. But the root user can
override this precaution and allow SetUID binaries to behave as expected within a Singularity container with the
--allow-setuid option like so:
$ sudo singularity shell --allow-setuid some_container.sif
4.2.3 --keep-privs
It is possible for an admin to set a different set of default capabilities or to reduce the default capabilities to zero for the
root user by setting the root default capabilities parameter in the singularity.conf file to file
or no respectively. If this change is in effect, the root user can override the singularity.conf file and enter the
container with full capabilities using the --keep-privs option.
$ sudo singularity exec --keep-privs library://centos ping -c 1 8.8.8.8
PING 8.8.8.8 (8.8.8.8) 56(84) bytes of data.
64 bytes from 8.8.8.8: icmp_seq=1 ttl=128 time=18.8 ms
--- 8.8.8.8 ping statistics ---
1 packets transmitted, 1 received, 0% packet loss, time 0ms
rtt min/avg/max/mdev = 18.838/18.838/18.838/0.000 ms
4.2.4 --drop-caps
By default, the root user has a full set of capabilities when they enter the container. You may choose to drop specific
capabilities when you initiate a container as root to enhance security.
For instance, to drop the ability for the root user to open a raw socket inside the container:
$ sudo singularity exec --drop-caps CAP_NET_RAW library://centos ping -c 1 8.8.8.8
ping: socket: Operation not permitted
The drop-caps option will also accept the case insensitive keyword all as an option to drop all capabilities when
entering the container.
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4.2.5 --security
The --security flag allows the root user to leverage security modules such as SELinux, AppArmor, and seccomp
within your Singularity container. You can also change the UID and GID of the user within the container at runtime.
For instance:
$ sudo whoami
root
$ sudo singularity exec --security uid:1000 my_container.sif whoami
david
To use seccomp to blacklist a command follow this procedure. (It is actually preferable from a security standpoint to
whitelist commands but this will suffice for a simple example.) Note that this example was run on Ubuntu and that
Singularity was installed with the libseccomp-dev and pkg-config packages as dependencies.
First write a configuration file. An example configuration file is installed with Singularity, normally at /usr/local/
etc/singularity/seccomp-profiles/default.json. For this example, we will use a much simpler
configuration file to blacklist the mkdir command.
{
"defaultAction": "SCMP_ACT_ALLOW",
"archMap": [
{
"architecture": "SCMP_ARCH_X86_64",
"subArchitectures": [
"SCMP_ARCH_X86",
"SCMP_ARCH_X32"
]
}
],
"syscalls": [
{
"names": [
"mkdir"
],
"action": "SCMP_ACT_KILL",
"args": [],
"comment": "",
"includes": {},
"excludes": {}
}
]
}
We’ll save the file at /home/david/no_mkdir.json. Then we can invoke the container like so:
$ sudo singularity shell --security seccomp:/home/david/no_mkdir.json my_container.sif
Singularity> mkdir /tmp/foo
Bad system call (core dumped)
Note that attempting to use the blacklisted mkdir command resulted in a core dump.
The full list of arguments accepted by the --security option are as follows:
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Singularity Container Documentation, Release 3.0
--security="seccomp:/usr/local/etc/singularity/seccomp-profiles/default.json"
--security="apparmor:/usr/bin/man"
--security="selinux:context"
--security="uid:1000"
--security="gid:1000"
--security="gid:1000:1:0" (multiple gids, first is always the primary group)
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