Singularity Container Ation User Guide 3.0
User Manual:
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Singularity Container Documentation
Release 3.0
User Docs
Nov 08, 2018
CONTENTS
1
2
3
Quick Start
1.1 Quick Installation Steps . . . . . . . . . . . . . . . . .
1.1.1
Install system dependencies . . . . . . . . . .
1.1.2
Install Go . . . . . . . . . . . . . . . . . . . .
1.1.3
Clone the Singularity repository . . . . . . . .
1.1.4
Install Go dependencies . . . . . . . . . . . . .
1.1.5
Compile the Singularity binary . . . . . . . . .
1.2 Overview of the Singularity Interface . . . . . . . . . .
1.3 Download pre-built images . . . . . . . . . . . . . . . .
1.4 Interact with images . . . . . . . . . . . . . . . . . . .
1.4.1
Shell . . . . . . . . . . . . . . . . . . . . . . .
1.4.2
Executing Commands . . . . . . . . . . . . . .
1.4.3
Running a container . . . . . . . . . . . . . . .
1.4.4
Working with Files . . . . . . . . . . . . . . .
1.5 Build images from scratch . . . . . . . . . . . . . . . .
1.5.1
Sandbox Directories . . . . . . . . . . . . . .
1.5.2
Converting images from one format to another .
1.5.3
Singularity Definition Files . . . . . . . . . . .
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1
1
1
1
2
2
2
2
4
5
5
6
6
7
8
8
8
9
Build a Container
2.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . .
2.2 Downloading an existing container from the Container Library
2.3 Downloading an existing container from Docker Hub . . . . .
2.4 Creating writable --sandbox directories . . . . . . . . . .
2.5 Converting containers from one format to another . . . . . . .
2.6 Building containers from Singularity definition files . . . . .
2.7 Build options . . . . . . . . . . . . . . . . . . . . . . . . . .
2.7.1 --builder . . . . . . . . . . . . . . . . . . . . .
2.7.2 --detached . . . . . . . . . . . . . . . . . . . .
2.7.3 --force . . . . . . . . . . . . . . . . . . . . . . .
2.7.4 --json . . . . . . . . . . . . . . . . . . . . . . . .
2.7.5 --library . . . . . . . . . . . . . . . . . . . . .
2.7.6 --notest . . . . . . . . . . . . . . . . . . . . . .
2.7.7 --remote . . . . . . . . . . . . . . . . . . . . . .
2.7.8 --sandbox . . . . . . . . . . . . . . . . . . . . .
2.7.9 --section . . . . . . . . . . . . . . . . . . . . .
2.7.10 --update . . . . . . . . . . . . . . . . . . . . . .
2.8 More Build topics . . . . . . . . . . . . . . . . . . . . . . .
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11
11
11
12
12
12
12
13
13
13
13
13
13
13
13
14
14
14
14
Bind Paths and Mounts
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15
i
3.1
3.2
3.3
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15
15
15
15
16
4
Persistent Overlays
4.1 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
4.2 Usage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
17
17
17
5
Signing and Verifying Containers
5.1 Verifying containers from the Container Library . .
5.2 Signing your own containers . . . . . . . . . . . . .
5.2.1
Generating and managing PGP keys . . . .
5.2.2
Signing and validating your own containers
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19
19
19
19
20
Security Options
6.1 Linux Capabilities . . . . . .
6.2 Security related action options
6.2.1 --add-caps . . .
6.2.2 --allow-setuid
6.2.3 --keep-privs . .
6.2.4 --drop-caps . . .
6.2.5 --security . . .
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23
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24
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24
25
Network virtualization
7.1 --dns . . . . . . .
7.2 --hostname . . .
7.3 --net . . . . . . .
7.4 --network . . . .
7.5 --network-args
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27
27
27
27
28
28
Limiting container resources with cgroups
8.1 Overview . . . . . . . . . . . . . . . . .
8.2 Examples . . . . . . . . . . . . . . . . .
8.2.1
Limiting memory . . . . . . . .
8.2.2
Limiting CPU . . . . . . . . . .
8.2.2.1 shares . . . . . . . . .
8.2.2.2 quota/period . . . . . .
8.2.2.3 cpus/mems . . . . . . .
8.2.3
Limiting IO . . . . . . . . . . .
8.2.3.1 Limiting device access .
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31
31
31
31
32
32
32
32
33
34
6
7
8
ii
Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
System-defined bind paths . . . . . . . . . . . . . . . . . . . .
User-defined bind paths . . . . . . . . . . . . . . . . . . . . .
3.3.1
Specifying bind paths . . . . . . . . . . . . . . . . . .
3.3.2
A note on using --bind with the --writable flag
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.
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 information 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
1
Singularity Container Documentation, Release 3.0
$ 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
-h, --help
-q, --quiet
-s, --silent
-t, --tokenfile string
-v, --verbose
print debugging information (highest verbosity)
help for singularity
suppress normal output
only print errors
path to the file holding your sylabs
authentication token (default
"/home/david/.singularity/sylabs-token")
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
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...]
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,
-h,
-i,
-u,
--groupid uint32
--help
--id uint32
--url string
group ID to be verified
help for verify
descriptor ID to be verified
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 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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TWO
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.
2.1 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.
2.2 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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2.3 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
2.4 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/
2.5 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 nonreproducible. It is a best practice to build your immutable production containers directly from a Singularity definition
file instead.
2.6 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
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%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.
2.7 Build options
2.7.1 --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.
2.7.2 --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.
2.7.3 --force
The --force option will delete and overwrite an existing Singularity image without presenting the normal interactive
prompt.
2.7.4 --json
The --json option will force Singularity to interpret a given definition file as a json.
2.7.5 --library
This command allows you to set a different library. (The default library is “https://library.sylabs.io”)
2.7.6 --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.
2.7.7 --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”.)
2.7. Build options
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2.7.8 --sandbox
Build a sandbox (chroot directory) instead of the default SIF format.
2.7.9 --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.
2.7.10 --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.
2.8 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
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CHAPTER
THREE
BIND PATHS AND MOUNTS
If enabled by the system administrator, Singularity allows you to map directories on your host system to directories
within your container using bind mounts. This allows you to read and write data on the host system with ease.
3.1 Overview
When Singularity ‘swaps’ the host operating system for the one inside your container, the host file systems becomes
inaccessible. But you may want to read and write files on the host system from within the container. To enable this
functionality, Singularity will bind directories back into the container via two primary methods: system-defined bind
paths and user-defined bind paths.
3.2 System-defined bind paths
The system administrator has the ability to define what bind paths will be included automatically inside each container.
Some bind paths are automatically derived (e.g. a user’s home directory) and some are statically defined (e.g. bind
paths in the Singularity configuration file). In the default configuration, the directories $HOME , /tmp , /proc ,
/sys , /dev, and $PWD are among the system-defined bind paths.
3.3 User-defined bind paths
If the system administrator has enabled user control of binds, you will be able to request your own bind paths within
your container.
The Singularity action commands (run, exec, shell, and instance start will accept the --bind/
-B command-line option to specify bind paths, and will also honor the $SINGULARITY_BIND (or
$SINGULARITY_BINDPATH) environment variable. The argument for this option is a comma-delimited string
of bind path specifications in the format src[:dest[:opts]], where src and dest are paths outside and inside
of the container respectively. If dest is not given, it is set equal to src. Mount options (opts) may be specified as
ro (read-only) or rw (read/write, which is the default). The --bind/-B option can be specified multiple times, or a
comma-delimited string of bind path specifications can be used.
3.3.1 Specifying bind paths
Here’s an example of using the --bind option and binding /data on the host to /mnt in the container (/mnt does
not need to already exist in the container):
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$ ls /data
bar foo
$ singularity exec --bind /data:/mnt my_container.sif ls /mnt
bar foo
You can bind multiple directories in a single command with this syntax:
$ singularity shell --bind /opt,/data:/mnt my_container.sif
This will bind /opt on the host to /opt in the container and /data on the host to /mnt in the container.
Using the environment variable instead of the command line argument, this would be:
$ export SINGULARITY_BIND="/opt,/data:/mnt"
$ singularity shell my_container.sif
Using the environment variable $SINGULARITY_BIND, you can bind paths even when you are running your container as an executable file with a runscript. If you bind many directories into your Singularity containers and they
don’t change, you could even benefit by setting this variable in your .bashrc file.
3.3.2 A note on using --bind with the --writable flag
To mount a bind path inside the container, a bind point must be defined within the container. The bind point is a
directory within the container that Singularity can use as a destination to bind a directory on the host system.
Starting in version 3.0, Singularity will do its best to bind mount requested paths into a container regardless of whether
the appropriate bind point exists within the container. Singularity can often carry out this operation even in the absence
of the “overlay fs” feature.
However, binding paths to non-existent points within the container can result in unexpected behavior when used in
conjuction with the --writable flag, and is therefore disallowed. If you need to specify bind paths in combination
with the --writable flag, please ensure that the appropriate bind points exist within the container. If they do not
already exist, it will be necessary to modify the container and create them.
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CHAPTER
FOUR
PERSISTENT OVERLAYS
Persistent overlay directories allow you to overlay a writable file system on an immutable read-only container for the
illusion of read-write access.
4.1 Overview
A persistent overlay is a directory that “sits on top” of your compressed, immutable SIF container. When you install
new software or create and modify files the overlay directory stores the changes.
If you want to use a SIF container as though it were writable, you can create a directory to use as a persistent overlay.
Then you can specify that you want to use the directory as an overlay at runtime with the --overlay option.
You can use a persistent overlays with the following commands:
• run
• exec
• shell
• instance.start
4.2 Usage
To use a persistent overlay, you must first have a container.
$ sudo singularity build ubuntu.sif library://ubuntu
Then you must create a directory. (You can also use the --overlay option with a legacy writable ext3 image.)
$ mkdir my_overlay
Now you can use this overlay directory with your container. Note that it is necessary to be root to use an overlay
directory.
$ sudo singularity shell --overlay my_overlay/ ubuntu.sif
Singularity ubuntu.sif:~> touch /foo
Singularity ubuntu.sif:~> apt-get update && apt-get install -y vim
Singularity ubuntu.sif:~> which vim
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/usr/bin/vim
Singularity ubuntu.sif:~> exit
You will find that your changes persist across sessions as though you were using a writable container.
$ sudo singularity shell --overlay my_overlay/ ubuntu.sif
Singularity ubuntu.sif:~> ls /foo
/foo
Singularity ubuntu.sif:~> which vim
/usr/bin/vim
Singularity ubuntu.sif:~> exit
If you mount your container without the --overlay directory, your changes will be gone.
$ sudo singularity shell ubuntu.sif
Singularity ubuntu.sif:~> ls /foo
ls: cannot access 'foo': No such file or directory
Singularity ubuntu.sif:~> which vim
Singularity ubuntu.sif:~> exit
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FIVE
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.
5.1 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 , KeyID 51BE5020C508C7E9
In this example you can see that Sylabs Admin has signed the container.
5.2 Signing your own containers
5.2.1 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)
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)
-------------------------------------------------------------------------------$ 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).
5.2.2 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) , 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) , 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.
5.2. Signing your own containers
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Chapter 5. Signing and Verifying Containers
CHAPTER
SIX
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.
6.1 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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6.2 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.
6.2.1 --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.
6.2.2 --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
6.2.3 --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
6.2.4 --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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6.2.5 --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:
6.2. Security related action options
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--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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CHAPTER
SEVEN
NETWORK VIRTUALIZATION
Singularity 3.0 introduces full integration with cni , and several new features to make network virtualization easy.
A few new options have been added to the action commands (exec, run, and shell) to facilitate these features, and
the --net option has been updated as well. These options can only be used by root.
7.1 --dns
The --dns option allows you to specify a comma separated list of DNS servers to add to the /etc/resolv.conf
file.
$ nslookup sylabs.io | grep Server
Server:
127.0.0.53
$ sudo singularity exec --dns 8.8.8.8 ubuntu.sif nslookup sylabs.io | grep Server
Server:
8.8.8.8
$ sudo singularity exec --dns 8.8.8.8 ubuntu.sif cat /etc/resolv.conf
nameserver 8.8.8.8
7.2 --hostname
The --hostname option accepts a string argument to change the hostname within the container.
$ hostname
ubuntu-bionic
$ sudo singularity exec --hostname hal-9000 my_container.sif hostname
hal-9000
7.3 --net
Passing the --net flag will cause the container to join a new network namespace when it initiates. New in Singularity
3.0, a bridge interface will also be set up by default.
$ hostname -I
10.0.2.15
(continues on next page)
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(continued from previous page)
$ sudo singularity exec --net my_container.sif hostname -I
10.22.0.4
7.4 --network
The --network option can only be invoked in combination with the --net flag. It accepts a comma delimited
string of network types. Each entry will bring up a dedicated interface inside container.
$ hostname -I
172.16.107.251 10.22.0.1
$ sudo singularity exec --net --network ptp ubuntu.sif hostname -I
10.23.0.6
$ sudo singularity exec --net --network bridge,ptp ubuntu.sif hostname -I
10.22.0.14 10.23.0.7
When invoked, the --network option searches the singularity configuration directory (commonly /usr/local/
etc/singularity/network/) for the cni configuration file corresponding to the requested network type(s).
Several configuration files are installed with Singularity by default corresponding to the following network types:
• bridge
• ptp
• ipvlan
• macvlan
Administrators can also define custom network configurations and place them in the same directory for the benefit of
users.
7.5 --network-args
The --network-args option provides a convenient way to specify arguments to pass directly to the cni plugins. It
must be used in conjuction with the --net flag.
For instance, let’s say you want to start an NGINX server on port 80 inside of the container, but you want to map it to
port 8080 outside of the container:
$ sudo singularity instance start --writable-tmpfs \
--net --network-args "portmap=8080:80/tcp" docker://nginx web2
The above command will start the Docker Hub official NGINX image running in a background instance called web2.
The NGINX instance will need to be able to write to disk, so we’ve used the --writable-tmpfs argument to allocate some space in memory. The --net flag is necessary when using the --network-args option, and specifying
the portmap=8080:80/tcp argument which will map port 80 inside of the container to 8080 on the host.
Now we can start NGINX inside of the container:
$ sudo singularity exec instance://web2 nginx
And the curl command can be used to verify that NGINX is running on the host port 8080 as expected.
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$ curl localhost:8080
10.22.0.1 - - [16/Oct/2018:09:34:25 -0400] "GET / HTTP/1.1" 200 612 "-" "curl/7.58.0"
˓→"-"
Welcome to nginx!
Welcome to nginx!
If you see this page, the nginx web server is successfully installed and
working. Further configuration is required.
For online documentation and support please refer to
nginx.org.
Commercial support is available at
nginx.com.
Thank you for using nginx.
For more information about cni, check the cni specification.
7.5. --network-args
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CHAPTER
EIGHT
LIMITING CONTAINER RESOURCES WITH CGROUPS
Starting in Singularity 3.0, users have the ability to limit container resources using cgroups.
8.1 Overview
Singularity cgroups support can be configured and utilized via a TOML file. An example file is typically installed
at /usr/local/etc/singularity/cgroups/cgroups.toml. You can copy and edit this file to suit your
needs. Then when you need to limit your container resources, apply the settings in the TOML file by using the path as
an argument to the --apply-cgroups option like so:
$ sudo singularity shell --apply-cgroups /path/to/cgroups.toml my_container.sif
The --apply-cgroups option can only be used with root privileges.
8.2 Examples
8.2.1 Limiting memory
To limit the amount of memory that your container uses to 500MB (524288000 bytes), follow this example. First,
create a cgroups.toml file like this and save it in your home directory.
[memory]
limit = 524288000
Start your container like so:
$ sudo singularity instance start --apply-cgroups /home/$USER/cgroups.toml \
my_container.sif instance1
After that, you can verify that the container is only using 500MB of memory. (This example assumes that instance1
is the only running instance.)
$ cat /sys/fs/cgroup/memory/singularity/*/memory.limit_in_bytes
524288000
After you are finished with this example, be sure to cleanup your instance with the following command.
$ sudo singularity instance stop instance1
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Similarly, the remaining examples can be tested by starting instances and examining the contents of the appropriate
subdirectories of /sys/fs/cgroup/.
8.2.2 Limiting CPU
Limit CPU resources using one of the following strategies. The cpu section of the configuration file can limit memory
with the following:
8.2.2.1 shares
This corresponds to a ratio versus other cgroups with cpu shares. Usually the default value is 1024. That means if
you want to allow to use 50% of a single CPU, you will set 512 as value.
[cpu]
shares = 512
A cgroup can get more than its share of CPU if there are enough idle CPU cycles available in the system, due to the
work conserving nature of the scheduler, so a contained process can consume all CPU cycles even with a ratio of 50%.
The ratio is only applied when two or more processes conflicts with their needs of CPU cycles.
8.2.2.2 quota/period
You can enforce hard limits on the CPU cycles a cgroup can consume, so contained processes can’t use more than the
amount of CPU time set for the cgroup. quota allows you to configure the amount of CPU time that a cgroup can
use per period. The default is 100ms (100000us). So if you want to limit amount of CPU time to 20ms during period
of 100ms:
[cpu]
period = 100000
quota = 20000
8.2.2.3 cpus/mems
You can also restrict access to specific CPUs and associated memory nodes by using cpus/mems fields:
[cpu]
cpus = "0-1"
mems = "0-1"
Where container has limited access to CPU 0 and CPU 1.
Note: It’s important to set identical values for both cpus and mems.
For more information about limiting CPU with cgroups, see the following external links:
• Red Hat resource management guide section 3.2 CPU
• Red Hat resource management guide section 3.4 CPUSET
• Kernel scheduler documentation
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8.2.3 Limiting IO
You can limit and monitor access to I/O for block devices. Use the [blockIO] section of the configuration file to do
this like so:
[blockIO]
weight = 1000
leafWeight = 1000
weight and leafWeight accept values between 10 and 1000.
weight is the default weight of the group on all the devices until and unless overridden by a per device rule.
leafWeight relates to weight for the purpose of deciding how heavily to weigh tasks in the given cgroup while
competing with the cgroup’s child cgroups.
To override weight/leafWeight for /dev/loop0 and /dev/loop1 block devices you would do something
like this:
[blockIO]
[[blockIO.weightDevice]]
major = 7
minor = 0
weight = 100
leafWeight = 50
[[blockIO.weightDevice]]
major = 7
minor = 1
weight = 100
leafWeight = 50
You could limit the IO read/write rate to 16MB per second for the /dev/loop0 block device with the following
configuration. The rate is specified in bytes per second.
[blockIO]
[[blockIO.throttleReadBpsDevice]]
major = 7
minor = 0
rate = 16777216
[[blockIO.throttleWriteBpsDevice]]
major = 7
minor = 0
rate = 16777216
To limit the IO read/write rate to 1000 IO per second (IOPS) on /dev/loop0 block device, you can do the following.
The rate is specified in IOPS.
[blockIO]
[[blockIO.throttleReadIOPSDevice]]
major = 7
minor = 0
rate = 1000
[[blockIO.throttleWriteIOPSDevice]]
major = 7
minor = 0
rate = 1000
For more information about limiting IO, see the following external links:
8.2. Examples
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• Red Hat resource management guide section 3.1 blkio
• Kernel block IO controller documentation
• Kernel CFQ scheduler documentation
8.2.3.1 Limiting device access
You can limit read, write, or creation of devices. In this example, a container is configured to only be able to read from
or write to /dev/null.
[[devices]]
access = "rwm"
allow = false
[[devices]]
access = "rw"
allow = true
major = 1
minor = 3
type = "c"
For more information on limiting access to devices the Red Hat resource management guide section 3.5 DEVICES.
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