Environment and Metadata

Environment variables are values you can set in a session, which can be used to influence the behavior of programs. It’s often considered best practice to use environment variables to pass settings to a program in a container, because they are easily set and don’t rely on writing and binding in program-specific configuration files. When building a container you may need to set fixed or default environment variables. When running containers you may need to set or override environment variables.

The metadata of a container is information that describes the container. SingularityCE automatically records important information such as the definition file used to build a container. Other details such as the version of SingularityCE used are present as labels on a container. You can also specify your own to be recorded against your container.

Changes in SingularityCE 3.6

SingularityCE 3.6 modified the ways in which environment variables are handled to allow long-term stability and consistency that has been lacking in prior versions. It also introduced new ways of setting environment variables, such as the --env and --env-file options.

Warning

If you have containers built with SingularityCE <3.6, and frequently set and override environment variables, please review this section carefully. Some behavior has changed.

Summary of changes

  • When building a container, the environment defined in the base image (e.g. a Docker image) is available during the %post section of the build.

  • An environment variable set in a container image, from the bootstrap base image, or in the %environment section of a definition file will not be overridden by a host environment variable of the same name. The --env, --env-file, or SINGULARITYENV_ methods must be used to explicitly override a environment variable set by the container image.

Environment Overview

When you run a program in a container with SingularityCE, the environment variables that the program sees are a combination of:

  • The environment variables set in the base image (e.g. Docker image) used to build the container.

  • The environment variables set in the %environment section of the definition file used to build the container.

  • Most of the environment variables set on your host, which are passed into the container.

  • Any variables you set specifically for the container at runtime, using the --env, --env-file options, or by setting SINGULARITYENV_ variables outside of the container.

  • The PATH variable can be manipulated to add entries.

  • Runtime variables SINGULARITY_xxx set by SingularityCE to provide information about the container.

The environment variables from the base image or definition file used to build a container always apply, but can be overridden.

You can choose to exclude passing environment variables from the host into the container with the -e or --cleanenv option.

We’ll go through each place environment variables can be defined, so that you can understand how the final environment in a container is created, and can be manipulated.

If you are interested in variables available when you are building a container, rather than when running a container, see build environment section.

Environment from a base image

When you build a container with SingularityCE you might bootstrap from a library or Docker image, or using Linux distribution bootstrap tools such as debootstrap, yum etc.

When using debootstrap, yum etc. you are starting from a fresh install of a Linux distribution into your container. No specific environment variables will be set. If you are using a library or Docker source then you may inherit environment variables from your base image.

If I build a singularity container from the image docker://python:3.7 then when I run the container I can see that the PYTHON_VERSION variable is set in the container:

$ singularity exec python.sif env | grep PYTHON_VERSION
PYTHON_VERSION=3.7.7

This happens because the Dockerfile used to build that container has ENV PYTHON_VERSION 3.7.7 set inside it.

You can always override the value of these base image environment variables, if needed. See below.

Environment from a definition file

Environment variables can be included in your container by adding them to your definition file. Use export in the %environment section of a definition file to set a container environment variable:

Bootstrap: library
From: default/alpine

%environment
    export MYVAR="Hello"

%runscript
    echo $MYVAR

Now the value of MYVAR is Hello when the container is launched. The %runscript is set to echo the value.

$ singularity run env.sif
Hello

Warning

SingularityCE 3.6 uses an embedded shell interpreter to evaluate and setup container environments, therefore all commands executed from the %environment section have an execution timeout of 5 seconds for SingularityCE 3.6 and a 1 minute timeout since SingularityCE 3.7. While it is fine to source a script from there, it is not recommended to use this section to run potentially long initialization tasks because this would impact users running the image and the execution could abort due to timeout.

Environment from the host

If you have environment variables set outside of your container, on the host, then by default they will be available inside the container. Except that:

  • The PS1 shell prompt is reset for a container specific prompt.

  • The PATH environment variable will be modified to contain default values.

  • The LD_LIBRARY_PATH is modified to a default /.singularity.d/libs, that will include NVIDIA / ROCm libraries if applicable.

Also, an environment variable set on the host will not override a variable of the same name that has been set inside the container image.

If you do not want the host environment variables to pass into the container you can use the -e or --cleanenv option. This gives a clean environment inside the container, with a minimal set of environment variables for correct operation of most software.

$ singularity exec --cleanenv env.sif env
HOME=/home/dave
LANG=C
LD_LIBRARY_PATH=/.singularity.d/libs
PATH=/startpath:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
PROMPT_COMMAND=PS1="Singularity> "; unset PROMPT_COMMAND
PS1=Singularity>
PWD=/home/dave/doc-tesrts
SINGULARITY_COMMAND=exec
SINGULARITY_CONTAINER=/home/dave/doc-tesrts/env.sif
SINGULARITY_ENVIRONMENT=/.singularity.d/env/91-environment.sh
SINGULARITY_NAME=env.sif
TERM=xterm-256color

Warning

If you work on a host system that sets a lot of environment variables, e.g. because you use software made available through environment modules / lmod, you may see strange behavior in your container. Check your host environment with env for variables such as PYTHONPATH that can change the way code runs, and consider using --cleanenv.

Environment from the SingularityCE runtime

It can be useful for a program to know when it is running in a SingularityCE container, and some basic information about the container environment. SingularityCE will automatically set a number of environment variables in a container that can be inspected by any program running in the container.

  • SINGULARITY_COMMAND - how the container was started, e.g. exec / run / shell.

  • SINGULARITY_CONTAINER - the full path to the container image.

  • SINGULARITY_ENVIRONMENT - path inside the container to the shell script holding the container image environment settings.

  • SINGULARITY_NAME - name of the container image, e.g. myfile.sif or docker://ubuntu.

  • SINGULARITY_BIND - a list of bind paths that the user requested, via flags or environment variables, when running the container.

Overriding environment variables

You can override variables that have been set in the container image, or define additional variables, in various ways as appropriate for your workflow.

--env option

New in SingularityCE 3.6

The --env option on the run/exec/shell commands allows you to specify environment variables as NAME=VALUE pairs:

$ singularity run env.sif
Hello

$ singularity run --env MYVAR=Goodbye env.sif
Goodbye

Separate multiple variables with commas, e.g. --env MYVAR=A,MYVAR2=B, and use shell quoting / shell escape if your variables include special characters.

--env-file option

New in SingularityCE 3.6

The --env-file option lets you provide a file that contains environment variables as NAME=VALUE pairs, e.g.:

$ cat myenvs
MYVAR="Hello from a file"

$ singularity run --env-file myenvs env.sif
Hello from a file

SINGULARITYENV_ prefix

If you export an environment variable on your host called SINGULARITYENV_xxx before you run a container, then it will set the environment variable xxx inside the container:

$ singularity run env.sif
Hello

$ export SINGULARITYENV_MYVAR="Overridden"
$ singularity run env.sif
Overridden

Manipulating PATH

PATH is a special environment variable that tells a system where to look for programs that can be run. PATH contains multiple filesystem locations (paths) separated by colons. When you ask to run a program myprog, the system looks through these locations one by one, until it finds myprog.

To ensure containers work correctly, when a host PATH might contain a lot of host-specific locations that are not present in the container, SingularityCE will ensure PATH in the container is set to a default.

/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

This covers the standard locations for software installed using a system package manager in most Linux distributions. If you have software installed elsewhere in the container, then you can override this by setting PATH in the container definition %environment block.

If your container depends on things that are bind mounted into it, or you have another need to modify the PATH variable when starting a container, you can do so with SINGULARITYENV_APPEND_PATH or SINGULARITYENV_PREPEND_PATH.

If you set a variable on your host called SINGULARITYENV_APPEND_PATH then its value will be appended (added to the end) of the PATH variable in the container.

$ singularity exec env.sif sh -c 'echo $PATH'
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

$ export SINGULARITYENV_APPEND_PATH="/endpath"
$ singularity exec env.sif sh -c 'echo $PATH'
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/endpath

Alternatively you could use the --env option to set a APPEND_PATH variable, e.g. --env APPEND_PATH=/endpath.

If you set a variable on your host called SINGULARITYENV_PREPEND_PATH then its value will be prepended (added to the start) of the PATH variable in the container.

$ singularity exec env.sif sh -c 'echo $PATH'
/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

$ export SINGULARITYENV_PREPEND_PATH="/startpath"
$ singularity exec env.sif sh -c 'echo $PATH'
/startpath:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin

Alternatively you could use the --env option to set a PREPEND_PATH variable, e.g. --env PREPEND_PATH=/startpath.

Evaluating container variables

When setting environment variables with --env etc. you can specify an escaped variable name, e.g. \$PATH to evaluate the value of that variable in the container.

For example, --env PATH="\$PATH:/endpath" would have the same effect as --env APPEND_PATH="/endpath".

Environment Variable Precedence

When a container is run with SingularityCE 3.6, the container environment is constructed in the following order:

  • Clear the environment, keeping just HOME and SINGULARITY_APPNAME.

  • Take Docker defined environment variables, where Docker was the base image source.

  • If PATH is not defined set the SingularityCE default PATH or

  • If PATH is defined, add any missing path parts from SingularityCE defaults

  • Take environment variables defined explicitly in the image (%environment). These can override any previously set values.

  • Set SCIF (--app) environment variables

  • Set base environment essential vars (PS1 and LD_LIBRARY_PATH)

  • Inject SINGULARITYENV_ / --env / --env-file variables so they can override or modify any previous values:

  • Source any remaining scripts from /singularity.d/env

Umask / Default File Permissions

The umask value on a Linux system controls the default permissions for newly created files. It is not an environment variable, but influences the behavior of programs in the container when they create new files.

Note

A detailed description of what the umask is, and how it works can be found at Wikipedia.

SingularityCE 3.7 and above set the umask in the container to match the value outside, unless:

  • The --fakeroot option is used, in which case a 0022 umask is set so that root owned newly created files have expected ‘system default’ permissions, and can be accessed by other non-root users who may use the same container later.

  • The --no-umask option is used, in which case a 0022 umask is set.

Note

In SingularityCE 3.6 and below a default 0022 umask was always applied.

Container Metadata

Each SingularityCE container has metadata describing the container, how it was built, etc. This metadata includes the definition file used to build the container and labels, which are specific pieces of information set automatically or explicitly when the container is built.

For containers that are generated with SingularityCE version 3.0 and later, default labels are represented using the rc1 Label Schema.

Inherited Labels

When building a container from an existing image, either directly from a URI or with a definition file, your container will inherit the labels that are set in that base image. For example the LABEL a Docker container sets in its Dockerfile, or a SIF container that sets labels in its definition file as described below.

Inherited labels can only be overwritten during a build when the build is performed using the --force option. SingularityCE will warn that it is not modifying an existing label when --force is not used:

$ singularity build test2.sif test2.def
...
INFO:    Adding labels
WARNING: Label: OWNER already exists and force option is false, not overwriting

Note

SingularityCE 3.0 through 3.8 did not inherit labels from Docker/OCI images during a build. SingularityCE 3.8 restores the behavior of 2.x, and inherits these labels.

Custom Labels

You can add custom labels to your container using the %labels section in a definition file:

Bootstrap: library
From: ubuntu:latest

%labels
  OWNER Joana

Dynamic Build Time Labels

You may wish to set a label to a value that is not known in advance, when you are writing the definition file, but can be obtained in the %post section of your definition file while the container is building.

SingularityCE 3.7 and above allow this, through adding labels to the file defined by the SINGULARITY_LABELS environment variable in the %post section:

Bootstrap: library
From: ubuntu:latest

# These labels take a fixed value in the definition
%labels
  OWNER Joana

# We can now also set labels to a value at build time
%post
  VAL="$(myprog --version)"
  echo "my.label $VAL" >> "$SINGULARITY_LABELS"

Labels must be added to the file one per line, in a NAME VALUE format, where the name and value are separated by a space.

Inspecting Metadata

The inspect command gives you the ability to view the labels and/or other metadata that were added to your container when it was built.

-l/ --labels

Running inspect without any options, or with the -l or --labels options will display any labels set on the container

$ singularity inspect ubuntu.sif
my.label: version 1.2.3
OWNER: Joana
org.label-schema.build-arch: amd64
org.label-schema.build-date: Thursday_12_November_2020_10:51:59_CST
org.label-schema.schema-version: 1.0
org.label-schema.usage.singularity.deffile.bootstrap: library
org.label-schema.usage.singularity.deffile.from: ubuntu:latest
org.label-schema.usage.singularity.version: 3.7.0-rc.1

We can easily see when the container was built, the source of the base image, and the exact version of SingularityCE that was used to build it.

The custom label OWNER that we set in our definition file is also visible.

-d / --deffile

The -d or -deffile flag shows the definition file(s) that were used to build the container.

$ singularity inspect --deffile jupyter.sif

And the output would look like:

Bootstrap: library
From: debian:9

%help
    Container with Anaconda 2 (Conda 4.5.11 Canary) and Jupyter Notebook 5.6.0 for Debian 9.x (Stretch).
    This installation is based on Python 2.7.15

%environment
    JUP_PORT=8888
    JUP_IPNAME=localhost
    export JUP_PORT JUP_IPNAME

%startscript
    PORT=""
    if [ -n "$JUP_PORT" ]; then
    PORT="--port=${JUP_PORT}"
    fi

    IPNAME=""
    if [ -n "$JUP_IPNAME" ]; then
    IPNAME="--ip=${JUP_IPNAME}"
    fi

    exec jupyter notebook --allow-root ${PORT} ${IPNAME}

%setup
    #Create the .condarc file where the environments/channels from conda are specified, these are pulled with preference to root
    cd /
    touch .condarc

%post
    echo 'export RANDOM=123456' >>$SINGULARITY_ENVIRONMENT
    #Installing all dependencies
    apt-get update && apt-get -y upgrade
    apt-get -y install \
    build-essential \
    wget \
    bzip2 \
    ca-certificates \
    libglib2.0-0 \
    libxext6 \
    libsm6 \
    libxrender1 \
    git
    rm -rf /var/lib/apt/lists/*
    apt-get clean
    #Installing Anaconda 2 and Conda 4.5.11
    wget -c https://repo.continuum.io/archive/Anaconda2-5.3.0-Linux-x86_64.sh
    /bin/bash Anaconda2-5.3.0-Linux-x86_64.sh -bfp /usr/local
    #Conda configuration of channels from .condarc file
    conda config --file /.condarc --add channels defaults
    conda config --file /.condarc --add channels conda-forge
    conda update conda
    #List installed environments
    conda list

Which is the definition file for the jupyter.sif container.

-r / --runscript

The -r or --runscript option shows the runscript for the image.

$ singularity inspect --runscript jupyter.sif

And the output would look like:

#!/bin/sh
OCI_ENTRYPOINT=""
OCI_CMD="bash"
# ENTRYPOINT only - run entrypoint plus args
if [ -z "$OCI_CMD" ] && [ -n "$OCI_ENTRYPOINT" ]; then
SINGULARITY_OCI_RUN="${OCI_ENTRYPOINT} $@"
fi

# CMD only - run CMD or override with args
if [ -n "$OCI_CMD" ] && [ -z "$OCI_ENTRYPOINT" ]; then
if [ $# -gt 0 ]; then
    SINGULARITY_OCI_RUN="$@"
else
    SINGULARITY_OCI_RUN="${OCI_CMD}"
fi
fi

# ENTRYPOINT and CMD - run ENTRYPOINT with CMD as default args
# override with user provided args
if [ $# -gt 0 ]; then
    SINGULARITY_OCI_RUN="${OCI_ENTRYPOINT} $@"
else
    SINGULARITY_OCI_RUN="${OCI_ENTRYPOINT} ${OCI_CMD}"
fi

exec $SINGULARITY_OCI_RUN

-t / --test

The -t or --test flag shows the test script for the image.

$ singularity inspect --test jupyter.sif

This will output the corresponding %test section from the definition file.

-e / --environment

The -e or --environment flag shows the environment variables that are defined in the container image. These may be set from one or more environment files, depending on how the container was built.

$ singularity inspect --environment jupyter.sif

And the output would look like:

==90-environment.sh==
#!/bin/sh

JUP_PORT=8888
JUP_IPNAME=localhost
export JUP_PORT JUP_IPNAME

-H / --helpfile

The -H or -helpfile flag will show the container’s description in the %help section of its definition file.

You can call it this way:

$ singularity inspect --helpfile jupyter.sif

And the output would look like:

Container with Anaconda 2 (Conda 4.5.11 Canary) and Jupyter Notebook 5.6.0 for Debian 9.x (Stretch).
This installation is based on Python 2.7.15

-j / --json

This flag gives you the possibility to output your labels in a JSON format.

You can call it this way:

$ singularity inspect --json ubuntu.sif

And the output would look like:

{
        "data": {
                "attributes": {
                        "labels": {
                                "my.label": "version 1.2.3",
                                "OWNER": "Joana",
                                "org.label-schema.build-arch": "amd64",
                                "org.label-schema.build-date": "Thursday_12_November_2020_10:51:59_CST",
                                "org.label-schema.schema-version": "1.0",
                                "org.label-schema.usage.singularity.deffile.bootstrap": "library",
                                "org.label-schema.usage.singularity.deffile.from": "ubuntu:latest",
                                "org.label-schema.usage.singularity.version": "3.7.0-rc.1"
                        }
                }
        },
        "type": "container"
}

/.singularity.d directory

The /.singularity.d directory in a container contains scripts and environment files that are used when a container is executed.

You should not manually modify files under /.singularity.d, from your definition file during builds, or directly within your container image. Recent 3.x versions of SingularityCE replace older action scripts dynamically, at runtime, to support new features. In the longer term, metadata will be moved outside of the container, and stored only in the SIF file metadata descriptor.

/.singularity.d/

├── actions
│   ├── exec
│   ├── run
│   ├── shell
│   ├── start
│   └── test
├── env
│   ├── 01-base.sh
|   ├── 10-docker2singularity.sh
│   ├── 90-environment.sh
│   ├── 91-environment.sh
|   ├── 94-appsbase.sh
│   ├── 95-apps.sh
│   └── 99-base.sh
├── labels.json
├── libs
├── runscript
├── runscript.help
├── Singularity
└── startscript
  • actions: This directory contains helper scripts to allow the container to carry out the action commands. (e.g. exec , run or shell). In later versions of SingularityCE, these files may be dynamically written at runtime, and should not be modified in the container.

  • env: All *.sh files in this directory are sourced in alphanumeric order when the container is started. For legacy purposes there is a symbolic link called /environment that points to /.singularity.d/env/90-environment.sh. Whenever possible, avoid modifying or creating environment files manually to prevent potential issues building & running containers with future versions of SingularityCE. Beginning with SingularityCE 3.6, additional facilities such as --env and --env-file are available to allow manipulation of the container environment at runtime.

  • labels.json: The json file that stores a containers labels described above.

  • libs: At runtime the user may request some host-system libraries to be mapped into the container (with the --nv option for example). If so, this is their destination.

  • runscript: The commands in this file will be executed when the container is invoked with the run command or called as an executable. For legacy purposes there is a symbolic link called /singularity that points to this file.

  • runscript.help: Contains the description that was added in the %help section.

  • SingularityCE: This is the definition file that was used to generate the container. If more than 1 definition file was used to generate the container additional SingularityCE files will appear in numeric order in a sub-directory called bootstrap_history.

  • startscript: The commands in this file will be executed when the container is invoked with the instance start command.