Admin Quick Start
This quick start gives an overview of installation of Singularity from source, a description of the architecture of Singularity, and pointers to configuration files. More information, including alternate installation options and detailed configuration options can be found later in this guide.
For additional help or support contact the Sylabs team.
Architecture of Singularity
Singularity is designed to allow containers to be executed as if they were native programs or scripts on a host system. No daemon is required to build or run containers, and the security model is compatible with shared systems.
As a result, integration with clusters and schedulers such as Univa Grid Engine, Torque, SLURM, SGE, and many others is as simple as running any other command. All standard input, output, errors, pipes, IPC, and other communication pathways used by locally running programs are synchronized with the applications running locally within the container.
Singularity favors an ‘integration over isolation’ approach to
containers. By default only the mount namespace is isolated for
containers, so that they have their own filesystem view. Access to
hardware such as GPUs, high speed networks, and shared filesystems is
easy and does not require special configuration. User home
directories, /tmp
space, and installation specific mounts make it
simple for users to benefit from the reproducibility of containerized
applications without major changs to their existing workflows. Where
more complete isolation is important, Singularity can use additional
Linux namespaces and other security and resource limits to accomplish
this.
Singularity Security
Singularity uses a number of strategies to provide safety and ease-of-use on both single-user and shared systems. Notable security features include:
The user inside a container is the same as the user who ran the container. This means access to files and devices from the container is easily controlled with standard POSIX permissions.
Container filesystems are mounted
nosuid
and container applications run with thePR_NO_NEW_PRIVS
flag set. This means that applications in a container cannot gain additional privileges. A regular user cannotsudo
or otherwise gain root privilege on the host via a container.The Singularity Image Format (SIF) supports encryption of containers, as well as cryptographic signing and verification of their content.
SIF containers are immutable and their payload is run directly, without extraction to disk. This means that the container can always be verified, even at runtime, and encrypted content is not exposed on disk.
Restrictions can be configured to limit the ownership, location, and cryptographic signatures of containers that are permitted to be run.
To support the SIF image format, automated networking setup etc., and
older Linux distributions without user namespace support, Singularity
runs small amounts of privileged container setup code via a
starter-setuid
binary. This is a ‘setuid root’ binary, so that
Singularity can perform filesystem loop mounts and other operations
that need privilege. The setuid flow is the default mode of operation,
but can be disabled on build, or in the
singularity.conf
configuration file if required.
Note
Running Singularity in non-setuid mode requires unprivileged user namespace support in the operating system kernel and does not support all features, most notably direct mounts of SIF images. This impacts integrity/security guarantees of containers at runtime.
See the non-setuid installation section for further detail on how to install singularity to run in non-setuid mode.
Installation from Source
Singularity Community Edition can be installed from source directly, or by building an RPM package from the source. Various Linux distributions also package Singularity, but their packages may not be up-to-date with the upstream version on GitHub.
To install Singularity directly from source, follow the procedure below. Other methods are discussed in the Installation section.
Note
This quick-start that you will install as root
using
sudo
, so that Singularity uses the default setuid
workflow, and all features are available. See the non-setuid
installation section of this guide for detail
of how to install as a non-root user, and how this affects the
functionality of Singularity.
Install Dependencies
On Red Hat Enterprise Linux or CentOS install the following dependencies:
$ sudo yum update -y && \
sudo yum groupinstall -y 'Development Tools' && \
sudo yum install -y \
openssl-devel \
libuuid-devel \
libseccomp-devel \
wget \
squashfs-tools \
cryptsetup
On Ubuntu or Debian install the following dependencies:
$ sudo apt-get update && sudo apt-get install -y \
build-essential \
uuid-dev \
libgpgme-dev \
squashfs-tools \
libseccomp-dev \
wget \
pkg-config \
git \
cryptsetup-bin
Install Go
Singularity v3 is written primarily in Go, and you will need Go 1.13 or above installed to compile it from source. Versions of Go packaged by your distribution may not be new enough to build Singularity.
The method below is one of several ways to install and configure Go.
Note
If you have previously installed Go from a download, rather than an
operating system package, you should remove your go
directory,
e.g. rm -r /usr/local/go
before installing a newer
version. Extracting a new version of Go over an existing
installation can lead to errors when building Go programs, as it
may leave old files, which have been removed or replaced in newer
versions.
Visit the Go download page and pick a package
archive to download. Copy the link address and download with wget. Then extract
the archive to /usr/local
(or use other instructions on go installation
page).
$ export VERSION=1.13.5 OS=linux ARCH=amd64 && \
wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
rm go$VERSION.$OS-$ARCH.tar.gz
Then, set up your environment for Go.
$ echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \
echo 'export PATH=/usr/local/go/bin:${PATH}:${GOPATH}/bin' >> ~/.bashrc && \
source ~/.bashrc
Download Singularity from a GitHub release
You can download Singularity from one of the releases. To see a full list, visit the GitHub release page. After deciding on a release to install, you can run the following commands to proceed with the installation.
$ export VERSION=3.6.4 && # adjust this as necessary \
wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-${VERSION}.tar.gz && \
tar -xzf singularity-${VERSION}.tar.gz && \
cd singularity
Compile & Install Singularity
Singularity uses a custom build system called makeit
. mconfig
is called
to generate a Makefile
and then make
is used to compile and install.
$ ./mconfig && \
make -C ./builddir && \
sudo make -C ./builddir install
By default Singularity will be installed in the /usr/local
directory
hierarchy. You can specify a custom directory with the --prefix
option, to
mconfig
:
$ ./mconfig --prefix=/opt/singularity
This option can be useful if you want to install multiple versions of Singularity, install a personal version of Singularity on a shared system, or if you want to remove Singularity easily after installing it.
For a full list of mconfig
options, run mconfig --help
. Here
are some of the most common options that you may need to use when
building Singularity from source.
--sysconfdir
: Install read-only config files in sysconfdir. This option is important if you need thesingularity.conf
file or other configuration files in a custom location.--localstatedir
: Set the state directory where containers are mounted. This is a particularly important option for administrators installing Singularity on a shared file system. The--localstatedir
should be set to a directory that is present on each individual node.-b
: Build Singularity in a given directory. By default this is./builddir
.
Configuration
Singularity is configured using files under etc/singularity
in
your --prefix
, or --syconfdir
if you used that option with
mconfig
. In a default installation from source without a
--prefix
set you will find them under
/usr/local/etc/singularity
.
You can edit these files directly, or using the singularity config
global
command as the root user to manage them.
singularity.conf
contains the majority of options controlling the
runtime behaviour of Singularity. Additional files control security,
network, and resource configuration. Head over to the
Configuration files section where the
files and configuration options are discussed.
Test Singularity
You can run a quick test of Singularity using a container in the Sylabs Container Library:
$ singularity exec library://alpine cat /etc/alpine-release
3.9.2
See the user guide for more information about how to use Singularity.