Support for Docker and OCI Containers

The Open Containers Initiative (OCI) container format, which grew out of Docker, is the dominant standard for cloud-focused containerized deployments of software. Although SingularityCE’s own container format has many unique advantages, it’s likely you will need to work with Docker/OCI containers at some point.

SingularityCE aims for maximum compatibility with Docker, within the constraints on a runtime that is well suited for use on shared systems and especially in HPC environments.

Using SingularityCE you can:

  • Pull, run, and build from most containers on Docker Hub, without changes.

  • Pull, run, and build from containers hosted on other registries, including private registries deployed on premise, or in the cloud.

  • Pull and build from OCI containers in archive formats, or cached in a local Docker daemon.

This section will highlight these workflows, and discuss the limitations and best practices to keep in mind when creating containers targeting both Docker and SingularityCE.

Containers From Docker Hub

Docker Hub is the most common place that projects publish public container images. At some point, it’s likely that you will want to run or build from containers that are hosted there.

Public Containers

It’s easy to run a public Docker Hub container with SingularityCE. Just put docker:// in front of the container repository and tag. To run the container that’s called sylabsio/lolcow:latest:

$ singularity run docker://sylabsio/lolcow:latest
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
Getting image source signatures
Copying blob 16ec32c2132b done
Copying blob 5ca731fc36c2 done
Copying config fd0daa4d89 done
Writing manifest to image destination
Storing signatures
2021/10/04 14:50:21  info unpack layer: sha256:16ec32c2132b43494832a05f2b02f7a822479f8250c173d0ab27b3de78b2f058
2021/10/04 14:50:23  info unpack layer: sha256:5ca731fc36c28789c5ddc3216563e8bfca2ab3ea10347e07554ebba1c953242e
INFO:    Creating SIF file...
 _____________________________
< Mon Oct 4 14:50:30 CDT 2021 >
 -----------------------------
        \   ^__^
         \  (oo)\_______
            (__)\       )\/\
                ||----w |
                ||     ||

Note that SingularityCE retrieves blobs and configuration data from Docker Hub, extracts the layers that make up the Docker container, and creates a SIF file from them. This SIF file is kept in your SingularityCE cache directory, so if you run the same Docker container again the downloads and conversion aren’t required.

To obtain the Docker container as a SIF file in a specific location, which you can move, share, and keep for later, singularity pull it:

$ singularity pull docker://sylabsio/lolcow
INFO:    Using cached SIF image

$ ls -l lolcow_latest.sif
-rwxr-xr-x 1 myuser myuser 74993664 Oct  4 14:55 lolcow_latest.sif

If it’s the first time you pull the container it’ll be downloaded and translated. If you have pulled the container before, it will be copied from the cache.

Note

singularity pull of a Docker container actually runs a singularity build behind the scenes, since we are translating from OCI to SIF. If you singularity pull a Docker container twice, the output file isn’t identical because metadata such as dates from the conversion will vary. This differs from pulling a SIF container (e.g. from a library:// URI), which always give you an exact copy of the image.

Docker Hub Limits

Docker Hub introduced limits on anonymous access to its API in November 2020. Every time you use a docker:// URI to run, pull etc. a container SingularityCE will make requests to Docker Hub in order to check whether the container has been modified there. On shared systems, and when running containers in parallel, this can quickly exhaust the Docker Hub API limits.

We recommend that you singularity pull a Docker image to a local SIF, and then always run from the SIF file, rather than using singularity run docker://... repeatedly.

Alternatively, if you have signed up for a Docker Hub account, make sure that you authenticate before using docker:// container URIs.

Authentication / Private Containers

To make use of the API limits under a Docker Hub account, or to access private containers, you’ll need to authenticate to Docker Hub. There are a number of ways to do this with SingularityCE.

Singularity CLI Remote Command

The singularity remote login command supports logging into Docker Hub and other OCI registries. For Docker Hub, the registry hostname is docker.io, so you will need to login as below, specifying your username:

$ singularity remote login --username myuser docker://docker.io
Password / Token:
INFO:    Token stored in /home/myuser/.singularity/remote.yaml

The Password / Token you enter must be a Docker Hub CLI access token, which you should generate in the ‘Security’ section of your account profile page on Docker Hub.

To check which Docker / OCI registries you are currently logged in to, use singularity remote list.

To logout of a registry, so that your credentials are forgotten, use singularity remote logout:

$ singularity remote logout docker://docker.io
INFO:    Logout succeeded

Docker CLI Authentication

If you have the docker CLI installed on your machine, you can docker login to your account. This stores authentication information in ~/.docker/config.json. The process that SingularityCE uses to retrieve Docker / OCI containers will attempt to use this information to login.

Note

SingularityCE can only read credentials stored directly in ~/.docker/config.json. It cannot read credentials from external Docker credential helpers.

Interactive Login

To perform a one-off interactive login, which will not store your credentials, use the --docker-login flag:

$ singularity pull --docker-login docker://sylabsio/private
Enter Docker Username: myuser
Enter Docker Password:

Environment Variables

When calling SingularityCE in a CI/CD workflow, or other non-interactive scenario, it may be useful to specify Docker Hub login credentials using environment variables. These are often the default way of passing secrets into jobs within CI pipelines.

Singularity accepts a username, and password / token, as SINGULARITY_DOCKER_USERNAME and SINGULARITY_DOCKER_PASSWORD respectively. These environment variables will override any stored credentials.

$ export SINGULARITY_DOCKER_USERNAME=myuser
$ export SINGULARITY_DOCKER_PASSWORD=mytoken
$ singularity pull docker://sylabsio/private

Containers From Other Registries

You can use docker:// URIs with SingularityCE to pull and run containers from OCI registries other than Docker Hub. To do this, you’ll need to include the hostname or IP address of the registry in your docker:// URI. Authentication with other registries is carried out in the same basic manner, but sometimes you’ll need to retrieve your credentials using a specific tool, especially when working with Cloud Service Provider environments.

Below are specific examples for some common registries. Most other registries follow a similar pattern for pulling public images, and authenticating to access private images.

Quay.io

Quay is an OCI container registry used by a large number of projects, and hosted at https://quay.io. To pull public containers from Quay, just include the quay.io hostname in your docker:// URI:

$ singularity pull docker://quay.io/bitnami/python:3.7
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...
...

$ singularity run python_3.7.sif
Python 3.7.12 (default, Sep 24 2021, 11:48:27)
[GCC 8.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>

To pull containers from private repositories you will need to generate a CLI token in the Quay web interface, then use it to login with SingularityCE. Use the same methods as described for Docker Hub above:

  • Run singularity remote login --username myuser docker://quay.io to store your credentials for SingularityCE.

  • Use docker login quay.io if docker is on your machine.

  • Use the --docker-login flag for a one-time interactive login.

  • Set the SINGULARITY_DOCKER_USERNAME and SINGULARITY_DOCKER_PASSWORD environment variables.

NVIDIA NGC

The NVIDIA NGC catalog at https://ngc.nvidia.com contains various GPU software, packaged in containers. Many of these containers are specifically documented by NVIDIA as supported by SingularityCE, with instructions available.

Previously, an account and API token was required to pull NGC containers. However, they are now available to pull as a guest without login:

$ singularity pull docker://nvcr.io/nvidia/pytorch:21.09-py3
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...

If you do need to pull containers using an NVIDIA account, e.g. if you have access to an NGC Private Registry, you will need to generate an API key in the web interface in order to authenticate.

Use one of the following authentication methods (detailed above for Docker Hub), with the username $oauthtoken and the password set to your NGC API key.

  • Run singularity remote login --username \$oauthtoken docker://nvcr.io to store your credentials for SingularityCE.

  • Use docker login nvcr.io if docker is on your machine.

  • Use the --docker-login flag for a one-time interactive login.

  • Set the SINGULARITY_DOCKER_USERNAME="\$oauthtoken" and SINGULARITY_DOCKER_PASSWORD environment variables.

See also: https://docs.nvidia.com/ngc/ngc-private-registry-user-guide/index.html

GitHub Container Registry

GitHub Container Registry is increasingly used to provide Docker containers alongside the source code of hosted projects. You can pull a public container from GitHub Container Registry using a ghcr.io URI:

$ singularity pull docker://ghcr.io/containerd/alpine:latest
INFO:    Converting OCI blobs to SIF format
INFO:    Starting build...

To pull private containers from GHCR you will need to generate a personal access token in the GitHub web interface in order to authenticate. This token must have required scopes. See the GitHub documentation here.

Use one of the following authentication methods (detailed above for Docker Hub), with your username and personal access token:

  • Run singularity remote login --username myuser docker://ghcr.io to store your credentials for SingularityCE.

  • Use docker login ghcr.io if docker is on your machine.

  • Use the --docker-login flag for a one-time interactive login.

  • Set the SINGULARITY_DOCKER_USERNAME and SINGULARITY_DOCKER_PASSWORD environment variables.

AWS ECR

To work with an AWS hosted Elastic Container Registry (ECR) generally requires authentication. There are various ways to generate credentials. You should follow one of the approaches in the ECR guide in order to obtain a username and password.

Warning

The ECR Docker credential helper cannot be used, as SingularityCE does not currently support external credential helpers used with Docker, only reading credentials stored directly in the .docker/config.json file.

The get-login-password approach is the most straightforward. It uses the AWS CLI to request a password, which can then be used to authenticate to an ECR private registry in the specified region. The username used in conjunction with this password is always AWS.

$ aws ecr get-login-password --region region

Then login using one of the following methods:

  • Run singularity remote login --username AWS docker://<accountid>.dkr.ecr.<region>.amazonaws.com to store your credentials for SingularityCE.

  • Use docker login --username AWS <accountid>.dkr.ecr.<region>.amazonaws.com if docker is on your machine.

  • Use the --docker-login flag for a one-time interactive login.

  • Set the SINGULARITY_DOCKER_USERNAME=AWS and SINGULARITY_DOCKER_PASSWORD environment variables.

You should now be able to pull containers from your ECR URI at docker://<accountid>.dkr.ecr.<region>.amazonaws.com.

Azure ACR

An Azure hosted Azure Container Registry (ACR) will generally hold private images and require authentication to pull from. There are several ways to authenticate to ACR, depending on the account type you use in Azure. See the ACR documentation for more information on these options.

Generally, for identities, using az acr login from the Azure CLI will add credentials to .docker/config.json which can be read by SingularityCE.

Service Principle accounts will have an explicit username and password, and you should authenticate using one of the following methods:

  • Run singularity remote login --username myuser docker://myregistry.azurecr.io to store your credentials for SingularityCE.

  • Use docker login --username myuser myregistry.azurecr.io if docker is on your machine.

  • Use the --docker-login flag for a one-time interactive login.

  • Set the SINGULARITY_DOCKER_USERNAME and SINGULARITY_DOCKER_PASSWORD environment variables.

The recent repository-scoped access token preview may be more convenient. See the preview documentation which details how to use az acr token create to obtain a token name and password pair that can be used to authenticate with the above methods.

Building From Docker / OCI Containers

If you wish to use an existing Docker or OCI container as the basis for a new container, you will need to specifiy it as the bootstrap source in a SingularityCE definition file.

Just as you can run or pull containers from different registries using a docker:// URI, you can use different headers in a definition file to instruct SingularityCE where to find the container you want to use as the starting point for your build.

Registries In Definition Files

When you wish to build from a Docker or OCI container that’s hosted in a registry, such as Docker Hub, your definition file should begin with Bootstrap: docker, followed with a From: line which specifies the location of the container you wish to pull.

Docker Hub

Docker Hub is the default registry, so when building from Docker Hub the From: header only needs to specify the container respository and tag:

Bootstrap: docker
From: ubuntu:20.04

If you singularity build a definition file with these lines, SingularityCE will fetch the ubuntu:20.04 container image from Docker Hub, and extract it as the basis for your new container.

Other Registries

To pull from a different Docker registry, you can either specify the hostname in the From: header, or use the separate Registry: header. The following two examples are equivalent:

Bootstrap: docker
From: quay.io/bitnami/python:3.7
Bootstrap: docker
Registry: quay.io
From: bitnami/python:3.7

Authentication During a Build

If you are building from an image in a private registry you will need to ensure that the credentials needed to access the image are available to SingularityCE.

A build might be run as the root user, e.g. via sudo, or under your own account with --fakeroot.

If you are running the build as root, using sudo, then any stored credentials or environment variables must be available to the root user:

  • Use the --docker-login flag for a one-time interactive login. I.E. run sudo singularity build --docker-login myimage.sif Singularity.

  • Set the SINGULARITY_DOCKER_USERNAME and SINGULARITY_DOCKER_PASSWORD environment variables. Pass the environment variables through sudo to the root build process by running sudo -E singularity build ....

  • Run sudo singularity remote login ... to store your credentials for the root user on your system. This is separate from storing the credentials under your own account.

  • Use sudo docker login if docker is on your machine. This is separate from storing the credentials under your own account.

If you are running the build under your account via the --fakeroot feature you do not need to specially set credentials for the root user.

Archives & Docker Daemon

As well as being hosted in a registry, Docker / OCI containers might be found inside a running Docker daemon, or saved as an archive. SingularityCE can build from these locations by using specialised bootstrap agents.

Containers Cached by the Docker Daemon

If you have pulled or run a container on your machine under docker, it will be cached locally by the Docker daemon. The docker images command will list containers that are available:

$ docker images
REPOSITORY          TAG                 IMAGE ID            CREATED             SIZE
sylabsio/lolcow     latest              5a15b484bc65        2 hours ago         188MB

This indicates that sylabsio/lolcow:latest has been cached locally by Docker. You can directly build it into a SIF file using a docker-daemon:// URI specifying the REPOSITORY:TAG container name:

$ singularity build lolcow_from_docker_cache.sif docker-daemon://sylabsio/lolcow:latest
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:a2022691bf950a72f9d2d84d557183cb9eee07c065a76485f1695784855c5193
 119.83 MiB / 119.83 MiB [==================================================] 6s
Copying blob sha256:ae620432889d2553535199dbdd8ba5a264ce85fcdcd5a430974d81fc27c02b45
 15.50 KiB / 15.50 KiB [====================================================] 0s
Copying blob sha256:c561538251751e3685c7c6e7479d488745455ad7f84e842019dcb452c7b6fecc
 14.50 KiB / 14.50 KiB [====================================================] 0s
Copying blob sha256:f96e6b25195f1b36ad02598b5d4381e41997c93ce6170cab1b81d9c68c514db0
 5.50 KiB / 5.50 KiB [======================================================] 0s
Copying blob sha256:7f7a065d245a6501a782bf674f4d7e9d0a62fa6bd212edbf1f17bad0d5cd0bfc
 3.00 KiB / 3.00 KiB [======================================================] 0s
Copying blob sha256:70ca7d49f8e9c44705431e3dade0636a2156300ae646ff4f09c904c138728839
 116.56 MiB / 116.56 MiB [==================================================] 6s
Copying config sha256:73d5b1025fbfa138f2cacf45bbf3f61f7de891559fa25b28ab365c7d9c3cbd82
 3.33 KiB / 3.33 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: lolcow_from_docker_cache.sif

The tag name must be included in the URI. Unlike when pulling from a registry, the docker-daemon bootstrap agent will not try to pull a latest tag automatically.

Note

In the example above, the build was performed without sudo. This is possible only when the user is part of the docker group on the host, since SingularityCE must contact the Docker daemon through its socket. If you are not part of the docker group you will need to use sudo for the build to complete successfully.

To build from an image cached by the Docker daemon in a definition file use Bootstrap: docker-daemon, and a From: <REPOSITORY>:TAG line:

Bootstrap: docker-daemon
From: sylabsio/lolcow:latest

Containers in Docker Archive Files

Docker allows containers to be exported into single file tar archives. These cannot be run directly, but are intended to be imported into Docker to run at a later date, or another location. SingularityCE can build from (or run) these archive files, by extracting them as part of the build process.

If an image is listed by the docker images command, then we can create a tar archive file using docker save and the image ID:

$ sudo docker images
REPOSITORY                        TAG               IMAGE ID       CREATED          SIZE
sylabsio/lolcow                   latest            5a15b484bc65   2 hours ago      188MB

$ docker save 5a15b484bc65 -o lolcow.tar

If we examine the contents of the tar file we can see that it contains the layers and metadata that make up a Docker container:

$ tar tvf lolcow.tar
drwxr-xr-x  0 0      0           0 Aug 16 11:22 2f0514a4c044af1ff4f47a46e14b6d46143044522fcd7a9901124209d16d6171/
-rw-r--r--  0 0      0           3 Aug 16 11:22 2f0514a4c044af1ff4f47a46e14b6d46143044522fcd7a9901124209d16d6171/VERSION
-rw-r--r--  0 0      0         401 Aug 16 11:22 2f0514a4c044af1ff4f47a46e14b6d46143044522fcd7a9901124209d16d6171/json
-rw-r--r--  0 0      0    75156480 Aug 16 11:22 2f0514a4c044af1ff4f47a46e14b6d46143044522fcd7a9901124209d16d6171/layer.tar
-rw-r--r--  0 0      0        1499 Aug 16 11:22 5a15b484bc657d2b418f2c20628c29945ec19f1a0c019d004eaf0ca1db9f952b.json
drwxr-xr-x  0 0      0           0 Aug 16 11:22 af7e389ea6636873dbc5adc17826e8401d96d3d384135b2f9fe990865af202ab/
-rw-r--r--  0 0      0           3 Aug 16 11:22 af7e389ea6636873dbc5adc17826e8401d96d3d384135b2f9fe990865af202ab/VERSION
-rw-r--r--  0 0      0         946 Aug 16 11:22 af7e389ea6636873dbc5adc17826e8401d96d3d384135b2f9fe990865af202ab/json
-rw-r--r--  0 0      0   118356480 Aug 16 11:22 af7e389ea6636873dbc5adc17826e8401d96d3d384135b2f9fe990865af202ab/layer.tar
-rw-r--r--  0 0      0         266 Dec 31  1969 manifest.json

We can convert this tar file into a singularity container using the docker-archive bootstrap agent. Because the agent accesses a file, rather than an object hosted by a service, it uses :<filename>, not ://<location>. To build a tar archive directly to a SIF container:

$ singularity build lolcow_tar.sif docker-archive:lolcow.tar
INFO:    Starting build...
Getting image source signatures
Copying blob sha256:2f0514a4c044af1ff4f47a46e14b6d46143044522fcd7a9901124209d16d6171
 119.83 MiB / 119.83 MiB [==================================================] 6s
Copying blob sha256:af7e389ea6636873dbc5adc17826e8401d96d3d384135b2f9fe990865af202ab
 15.50 KiB / 15.50 KiB [====================================================] 0s
Copying config sha256:5a15b484bc657d2b418f2c20628c29945ec19f1a0c019d004eaf0ca1db9f952b
 3.33 KiB / 3.33 KiB [======================================================] 0s
Writing manifest to image destination
Storing signatures
INFO:    Creating SIF file...
INFO:    Build complete: lolcow_tar.sif

Note

The docker-archive bootstrap agent can also handle gzipped Docker archives (.tar.gz or .tgz files).

To build an image using a definition file, which starts from a container in a Docker archive, use Bootstrap: docker-archive and specify the filename in the From: line:

Bootstrap: docker-archive
From: lolcow.tar

Differences and Limitations vs Docker

Though Docker / OCI container compatibility is a goal of SingularityCE, there are some differences and limitations due to the way SingularityCE was designed to work well on shared systems and HPC clusters. If you are having difficulty running a specific Docker container, check through the list of differences below. There are workarounds for many of the issues that you are most likely to face.

Read-only by Default

SingularityCE’s container image format (SIF) is generally read-only. This permits containers to be run in parallel from a shared location on a network filesystem, support in-built signing and verification, and offer encryption. A container’s filesystem is mounted directly from the SIF, as SquashFS, so cannot be written to by default.

When a container is run using Docker its layers are extracted, and the resulting container filesystem can be written to and modified by default. If a Docker container expects to write files, you will need to follow one of the following methods to allow it to run under SingularityCE.

  • A directory from the host can be passed into the container with the --bind or --mount flags. It needs to be mounted inside the container at the location where files will be written.

  • The --writable-tmpfs flag can be used to allow files to be created in a special temporary overlay. Any changes are lost when the container exits. The SIF file is never modified.

  • The container can be converted to a sandbox directory, and executed with the --writable flag, which allows modification of the sandbox content.

  • A writable overlay partition can be added to the SIF file, and the container executed with the --writable flag. Any changes made are kept permanently in the overlay partition.

Of these methods, only --writable-tmpfs is always safe to run in parallel. Each time the container is executed, a separate temporary overlay is used and then discarded.

Binding a directory into a container, or running a writable sandbox may or may not be safe, depending on the program executed. The program must use, and the filesystem support, some type of locking in order that the parallel runs do not interfere.

A writable overlay file in a SIF partition cannot be used in parallel. SingularityCE will refuse to run concurrently using the same SIF writable overlay partition.

Dockerfile USER

The Dockerfile used to build a Docker container may contain a USER statement. This tells the container runtime that it should run the container under the specified user account.

Because SingularityCE is designed to provide easy and safe access to data on the host system, work under batch schedulers, etc., it does not permit changing the user account the container is run as.

Any USER statement in a Dockerfile will be ignored by SingularityCE when the container is run. In practice, this often does not affect the execution of the software in the container. Software that is written in a way that requires execution under a specific user account will generally require modification for use with SingularityCE.

SingularityCE’s --fakeroot mode will start a container as a fake root user, mapped to the user’s real account outside of the container. Inside the container it is possible to change to another user account, which is mapped to a configured range of sub-uids / gids belonging to the original user. It may be possible to execute software expecting a fixed user account manually inside a --fakeroot shell, if your adminstrator has configured the system for --fakeroot.

Default Mounts / $HOME

A default installation of SingularityCE will mount the user’s home directory, /tmp directory, and the current working directory, into each container that is run. Administrators may also configure e.g. HPC project directories to automatically bind mount. Docker does not mount host directories into the container by default.

The home directory mount is the most likely to cause problems when running Docker containers. Various software will look for packages, plugins, and configuration files in $HOME. If you have, for example, installed packages for Python into your home directory (pip install --user) then a Python container may find and attempt to use them. This can cause conflicts and unexpected behaviour.

If you experience issues, use the --contain option to stop SingularityCE automatically binding directories into the container. You may need to use --bind or --mount to then add back e.g. an HPC project directory that you need access to.

# Without --contain, python in the container finds packages
# in your $HOME directory.
$ singularity exec docker://python:3.9 pip list
Package    Version
---------- -------
pip        21.2.4
rstcheck   3.3.1
setuptools 57.5.0
wheel      0.37.0

# With --contain, python in the container only finds packages
# installed in the container.
$ singularity exec --contain docker://python:3.9 pip list
Package    Version
---------- -------
pip        21.2.4
setuptools 57.5.0
wheel      0.37.0

Environment Propagation

SingularityCE propagates most environment variables set on the host into the container, by default. Docker does not propagate any host environment variables into the container. Environment variables may change the behaviour of software.

To disable automatic propagation of environment variables, the --cleanenv / -e flag can be specified. When --cleanenv is used, only variables on the host that are prefixed with SINGULARITYENV_ are set in the container:

# Set a host variable
$ export HOST_VAR=123
# Set a singularity container environment variable
$ export "SINGULARITYENV_FORCE_VAR="123"

$ singularity run library://alpine env | grep VAR
FORCE_VAR=123
HOST_VAR=ABC

$ singularity run --cleanenv library://alpine env | grep VAR
FORCE_VAR=123

Any environment variables set via an ENV line in a Dockerfile will be available when the container is run with SingularityCE.

Namespace & Device Isolation

Because SingularityCE favors an integration over isolation approach it does not, by default, use all the methods through which a container can be isolated from the host system. This makes it much easier to run a SingularityCE container like any other program, while the unique security model ensures safety. You can access the host’s network, GPUs, and other devices directly. Processes in the container are not numbered separately from host processes. Hostnames are not changed, etc.

Most containers are not impacted by the differences in isolation. If you require more isolation, than SingularityCE provides by default, you can enable some of the extra namespaces that Docker uses, with flags:

  • --ipc / -i creates a separate IPC (inter process communication) namespace, for SystemV IPC objects and POSIX message queues.

  • --net / -n creates a new network namespace, abstracting the container networking from the host.

  • --userns / -u runs the container unprivileged, inside a user namespace and avoiding setuid setup code. This prevents executing SIF images directly. They will be extracted to a directory sandbox.

  • --uts creates a new UTS namespace, which allows a different hostname and/or NIS domain for the container.

To limit presentation of devices from the host into the container, use the --contain flag. As well as preventing automatic binds of host directories into the container, --contain sets up a minimal /dev directory, rather than binding in the entire host /dev tree.

Note

When using the --nv or --rocm flags, GPU devices are present in the container even when --contain is used.

Init Shim Process

When a SingularityCE container is run using the --pid / p option, or started as an instance (which implies --pid), a shim init process is executed that will run the container payload itself.

The shim process helps to ensure signals are propagated correctly from the terminal, or batch schedulers etc. when containers are not designed for interactive use. Because Docker does not provide an init process by default, some containers have been designed to run their own init process, which cannot operate under the control of SingularityCE’s shim.

For example, a container using the tini init process will produce warnings when started as an instance, or if run with --pid. To work around this, use the --no-init flag to disable the shim:

$ singularity run --pid tini_example.sif
[WARN  tini (2690)] Tini is not running as PID 1 .
Zombie processes will not be re-parented to Tini, so zombie reaping won't work.
To fix the problem, run Tini as PID 1.

$ singularity run --pid --no-init tini_example.sif
...
# NO WARNINGS

Docker-like --compat Flag

If Docker-like behavior is important, SingularityCE can be started with the --compat flag. This flag is a convenient short-hand alternative to using all of:

  • --containall

  • --no-init

  • --no-umask

  • --writable-tmpfs

A container run with --compat has:

  • A writable root filesystem, using a temporary overlay where changes are discarded at container exit.

  • No automatic bind mounts of $HOME or other directories from the host into the container.

  • Empty temporary $HOME and /tmp directories, the contents of which will be discarded at container exit.

  • A minimal /dev tree, that does not expose host devices inside the container (except GPUs when used with --nv or --rocm).

  • An clean environment, not including environment variables set on the host.

  • Its own PID and IPC namespaces.

  • No shim init process.

These options will allow most, but not all, Docker / OCI containers to execute correctly under SingularityCE. The user namespace and network namespace are not used, as these negate benefits of SIF and direct access to high performance cluster networks.

CMD / ENTRYPOINT Behaviour

When a container is run using docker, its default behavior depends on the CMD and/or ENTRYPOINT set in the Dockerfile that was used to build it, along with any arguments on the command line. The CMD and ENTRYPOINT can also be overridden by flags.

A SingularityCE container has the concept of a runscript, which is a single shell script defining what happens when you singularity run the container. Because there is no internal concept of CMD and ENTRYPOINT, SingularityCE must create a runscript from the CMD and ENTRYPOINT when converting a Docker container. The behavior of this script mirrors Docker as closely as possible.

If the Docker container only has an ENTRYPOINT - that ENTRYPOINT is run, with any arguments appended:

# ENTRYPOINT="date"

# Runs 'date'
$ singularity run mycontainer.sif
Wed 06 Oct 2021 02:42:54 PM CDT

# Runs 'date --utc`
$ singularity run mycontainer.sif --utc
Wed 06 Oct 2021 07:44:27 PM UTC

If the Docker container only has a CMD - the CMD is run, or is replaced with any arguments:

# CMD="date"

# Runs 'date'
$ singularity run mycontainer.sif
Wed 06 Oct 2021 02:45:39 PM CDT

# Runs 'echo hello'
$ singularity run mycontainer.sif echo hello
hello

If the Docker container has a CMD and ENTRYPOINT, then we run ENTRYPOINT with either CMD as default arguments, or replaced with any user supplied arguments:

# ENTRYPOINT="date"
# CMD="--utc"

# Runs 'date --utc'
$ singularity run mycontainer.sif
Wed 06 Oct 2021 07:48:43 PM UTC

# Runs 'date -R'
$ singularity run mycontainer.sif -R
Wed, 06 Oct 2021 14:49:07 -0500

There is no flag to override an ENTRYPOINT set for a Docker container. Instead, use singularity exec to run an arbitrary program inside a container.

Best Practices for Docker & SingularityCE Compatibility

As detailed previously, SingularityCE can make use of most Docker and OCI images without issues, or via simple workarounds. In general, however, there are some best practices that should be applied when creating Docker / OCI containers that will also be run using SingularityCE.

  1. Don’t require execution by a specific user

Avoid using the USER instruction in your Docker file, as it is ignored by Singularity. Install and configure software inside the container so that it can be run by any user.

  1. Don’t install software under /root or in another user’s home directory

Because a Docker container builds and runs as the root user by default, it’s tempting to install software into root’s home directory (/root). Permissions on /root are usually set so that it is inaccessible to non-root users. When the container is run as another user the software may be inaccessible.

Software inside another user’s home directory, e.g. /home/myapp, may be obscured by SingularityCE’s automatic mounts onto /home.

Install software into system-wide locations in the container, such as under /usr or /opt to avoid these issues.

  1. Support a read-only filesystem

Because of the immutable nature of the SIF format, a container run with SingularityCE is read-only by default.

Try to ensure your container will run with a read-only filesystem. If this is not possible, document exactly where the container needs to write, so that a user can bind in a writable location, or use --writable-tmpfs as appropriate.

You can test read-only execution with Docker using docker run --read-only --tmpfs /run --tmpfs /tmp sylabsio/lolcow.

  1. Be careful writing to /tmp

SingularityCE mounts the host /tmp into the container, by default. This means you must be be careful when writing sensitive information to /tmp, and should ensure your container cleans up files it writes there.

  1. Consider library caches / ldconfig

If your Dockerfile adds libraries and / or manipulates the ld search path in the container (ld.so.conf / ld.so.conf.d), you should ensure the library cache is updated during the build.

Because Singularity runs containers read-only by default, the cache and any missing library symlinks may not be able to be updated / created at execution time.

Run ldconfig toward the end of your Dockerfile to ensure symbolic links and the the ld.so.cache are up-to-date.

Troubleshooting

Registry Authentication Issues

If you experience problems pulling containers from a private registry, check your credentials carefully. You can singularity pull with the --docker-login flag to perform an interactive login. This may be useful if you are unsure whether you have stored credentials properly via singularity remote login or docker login.

OCI registries expect different values for username and password fields. Some require a token to be generated and used instead of your account password. Some take a generic username, and rely only on the token to identify you. Consult the documentation for your registry carefully. Look for instructions that detail how to login via docker login without external helper programs, if possible.

Container Doesn’t Start

If a Docker container fails to start, the most common cause is that it needs to write files, while SingularityCE runs read-only by default.

Try running with the --writable-tmpfs option, or the --compat flag (which enables additional compatibility fixes).

You can also look for error messages mentioning ‘permission denied’ or ‘read-only filesystem’. Note where the program is attempting to write, and use --bind or --mount to bind a directory from the host system into that location. This will allow the container to write the needed files, which will appear in the directory you bind in.

Unexpected Container Behaviour

If a Docker container runs, but exhibits unexpected behavior, the most likely cause is the different level of isolation that Singularity provides vs Docker.

Try running the container with the --contain option, or the --compat option (which is more strict). This disables the automatic mount of your home directory, which is a common source of issues where software in the container loads configuration or packages that may be present there.

Getting Help

The community Slack channels and mailing list are excellent places to ask for help with running a specific Docker container. Other users may have already had success running the same container or software. Please don’t report issues with specific Docker containers on GitHub, unless you believe they are due to a bug in SingularityCE.

SingularityCE Definition file vs. Dockerfile

An alternative to running Docker containers with SingularityCE is to re-write the Dockerfile as a definition file, and build a native SIF image.

The table below gives a quick reference comparing Dockerfile and SingularityCE definition files. For more detail please see Definition Files.

SingularityCE Definition file

Dockerfile

Section

Description

Section

Description

Bootstrap

Defines the source of
the base image to build
your container from.
Many bootstrap agents
are supported, e.g.
library, docker,
http, shub,
yum, debootstrap.

-

Can only bootstrap
from Docker Hub.

From:

Specifies the base
image from which to the
build the container.

FROM

Creates a layer from
the specified docker image.

%setup

Run setup commands
outside of the
container (on the host
system) after the base
image bootstrap.

-

Not supported.

%files

Copy files from
your host to
the container, or
between build stages.

COPY

Copy files from
your host to
the container, or
between build stages.

%environment

Declare and set
container environment
variables.

ENV

Declare and set
a container environment
variable.

%help

Provide a help
section for your
container image.

-

Not supported.

%post

Commands that will
be run at
build-time.

RUN

Commands that will
be run at
build-time.

%runscript`

Commands that will
be run when you
singularity run
the container image.

ENTRYPOINT CMD

Commands / arguments
that will run in the
container image.

%startscript

Commands that will
be run when
an instance is started.

-

Not Applicable.

%test

Commands that run
at the very end
of the build process
to validate the
container using
a method of your
choice. (to verify
distribution or
software versions
installed inside
the container)

HEALTHCHECK

Commands that verify
the health status of
the container.

%apps

Allows you to install
internal modules
based on the concept
of SCIF-apps.

-

Not supported.

%labels

Section to add and
define metadata
describing your
container.

LABEL

Declare container
metadata as a
key-value pair.