Generating container recipes & images

EasyBuild has support for generating container recipes that will use EasyBuild to build and install a specified software stack. In addition, EasyBuild can (optionally) leverage the build tool provided by the container software of choice to create container images.

Note

The features documented here have been available since EasyBuild v3.6.0 but are still experimental, which implies they are subject to change in upcoming versions of EasyBuild.

You will need to enable the --experimental configuration option in order to use them. See Experimental features for more information.

For now (since EasyBuild v3.6.0), only Singularity (http://singularity.lbl.gov/) is supported.

Requirements

Usage

Generating container recipes (--containerize / -C)

To generate container recipes, use eb --containerize, or eb -C for short.

The resulting container recipe will, in turn, leverage EasyBuild to build and install the software that corresponds to the easyconfig files that are specified as arguments to the eb command (and all required dependencies, if needed).

Note

EasyBuild will refuse to overwrite existing container recipes.

To re-generate an already existing recipe file, use the --force command line option.

Base container image (--container-base)

In order to let EasyBuild generate a container recipe, it is required to specify which container image should be used as a base, via the --container-base configuration option.

Currently, three types of container base images can be specified:

  • localimage:<path>: the location of an existing container image file
  • docker:<name>: the name of a Docker container image (to be downloaded from Docker Hub, https://hub.docker.com/)
  • shub:<name>: the name of a Singularity container image (to be downloaded from Singularity Hub, https://singularity-hub.org/)

For the docker and shub types, an additional tag can be specified: docker:<name>:<tag> or shub:<name>:<tag>.

Note

You can also instruct EasyBuild which container base image should be used via the $EASYBUILD_CONTAINER_BASE environment variable, or by specifying container-base in an EasyBuild configuration file; see Supported configuration types.

Note

EasyBuild currently does not (yet) support generating a container recipe that results in a container image that is built from scratch, this will be implemented in a future version of EasyBuild.

To get started quickly, we recommend using one of the container base images available from https://singularity-hub.org/collections/143.

Requirements for base container image

There are a couple of specific requirements for the base container image:

  • all dependencies of EasyBuild must be installed, incl. Lmod (cfr. Requirements)
  • a user named easybuild must be available
  • the /scratch and /app directories must exist, and the easybuild user must have write permissions to those directories

The easybuild user will be used when running EasyBuild to install the specified software stack.

Note

The generated container recipe currrently hardcodes some of this. We intend to make this more configurable in a future version of EasyBuild.

Building container images (--container-build-image)

To instruct EasyBuild to also build a container image from the generated container recipe, use --container-build-image (in combination with -C or --containerize).

EasyBuild will leverage functionality provided by the container software of choice (see containers_cfg_image_type) to build the container image.

For example, in the case of Singularity, EasyBuild will run sudo /path/to/singularity build on the generated container recipe.

Note

In order to leverage the image building functionality of the container software, admin privileges are typically required. Therefore, EasyBuild will run the command to build the container image with sudo. You may need to enter your password to let the command execute.

EasyBuild will only run the actual container image build command with sudo. It will not use elevated privileges for anything else.

In case of doubt, you can use --extended-dry-run or -x do perform a dry run, so you can evaluate which commands will be executed (see also Extended dry run).

If you’re not comfortable with this, you can just let EasyBuild generate the container recipe, and then use that to build the actual container images yourself, either locally or through Singularity Hub (https://singularity-hub.org).

The container image will be placed in the location specified by the --containerpath configuration option (see Location for generated container recipes & images (--containerpath)), next to the generated container recipe that was used to build the image.

Note

When building container images, make sure to use a file system location with sufficient available storage space. Singularity may pull metadata during the build, and each image can range from several hundred MBs to GBs, depending on software stack you are including in the container image.

Note

EasyBuild will refuse to overwrite existing container images.

To re-generate an already existing image file, use the --force command line option.

Example usage

In this example, we will use a pre-built base container image located at /tmp/example.simg (see also Base container image (--container-base)).

To let EasyBuild generate a container recipe for GCC 6.4.0 + binutils 2.28:

eb GCC-6.4.0-2.28.eb --containerize --container-base localimage:/tmp/example.simg --experimental

With other configuration options left to default (see output of eb --show-config), this will result in a Singularity container recipe using example.simg as base image, which will be stored in $HOME/.local/easybuild/containers:

$ eb GCC-6.4.0-2.28.eb --containerize --container-base localimage:/tmp/example.simg --experimental
== temporary log file in case of crash /tmp/eb-dLZTNF/easybuild-LPLeG0.log
== Singularity definition file created at /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28
== Temporary log file(s) /tmp/eb-dLZTNF/easybuild-LPLeG0.log* have been removed.
== Temporary directory /tmp/eb-dLZTNF has been removed.

Example of a generated container recipe

Below is an example of container recipe for that was generated by EasyBuild, using the following command:

eb Python-3.6.4-foss-2018a.eb OpenMPI-2.1.2-GCC-6.4.0-2.28.eb -C --container-base shub:shahzebsiddiqui/eb-singularity:centos-7.4.1708 --experimental

It uses the shahzebsiddiqui/eb-singularity:centos-7.4.1708 base container image that is available from Singularity hub (see https://singularity-hub.org/collections/143).

Bootstrap: shub
From: shahzebsiddiqui/eb-singularity:centos-7.4.1708

%post
yum --skip-broken -y install openssl-devel libssl-dev libopenssl-devel
yum --skip-broken -y install libibverbs-dev libibverbs-devel rdma-core-devel


# upgrade easybuild package automatically to latest version
pip install -U easybuild

# change to 'easybuild' user
su - easybuild

eb Python-3.6.4-foss-2018a.eb OpenMPI-2.1.2-GCC-6.4.0-2.28.eb --robot --installpath=/app/ --prefix=/scratch --tmpdir=/scratch/tmp

# exit from 'easybuild' user
exit

# cleanup
rm -rf /scratch/tmp/* /scratch/build /scratch/sources /scratch/ebfiles_repo

%runscript
eval "$@"

%environment
source /etc/profile
module use /app/modules/all
module load Python/3.6.4-foss-2018a OpenMPI/2.1.2-GCC-6.4.0-2.28

%labels

Note

We also specify the easyconfig file for the OpenMPI component of foss/2018a here, because it requires specific OS dependencies to be installed (see the 2nd yum ... install line in the generated container recipe).

We intend to let EasyBuild take into account the OS dependencies of the entire software stack automatically in a future update.

The generated container recipe includes pip install -U easybuild to ensure that the latest version of EasyBuild is used to build the software in the container image, regardless of whether EasyBuild was already present in the container and which version it was.

In addition, the generated module files will follow the default module naming scheme (EasyBuildMNS). The modules that correspond to the easyconfig files that were specified on the command line will be loaded automatically, see the statements in the %environment section of the generated container recipe.

Example of building container image

You can instruct EasyBuild to also build the container image by also using --container-build-image.

Note that you will need to enter your sudo password (unless you recently executed a sudo command in the same shell session):

$ eb GCC-6.4.0-2.28.eb --containerize --container-base localimage:/tmp/example.simg --container-build-image --experimental
== temporary log file in case of crash /tmp/eb-aYXYC8/easybuild-8uXhvu.log
== Singularity tool found at /usr/bin/singularity
== Singularity version '2.4.6' is 2.4 or higher ... OK
== Singularity definition file created at /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28
== Running 'sudo /usr/bin/singularity build  /home/example/.local/easybuild/containers/GCC-6.4.0-2.28.simg /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28', you may need to enter your 'sudo' password...
== (streaming) output for command 'sudo /usr/bin/singularity build  /home/example/.local/easybuild/containers/GCC-6.4.0-2.28.simg /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28':
Using container recipe deffile: /home/example/.local/easybuild/containers/Singularity.GCC-6.4.0-2.28
Sanitizing environment
Adding base Singularity environment to container
...
== temporary log file in case of crash /scratch/tmp/eb-WnmCI_/easybuild-GcKyY9.log
== resolving dependencies ...
...
== building and installing GCCcore/6.4.0...
...
== building and installing binutils/2.28-GCCcore-6.4.0...
...
== building and installing GCC/6.4.0-2.28...
...
== COMPLETED: Installation ended successfully
== Results of the build can be found in the log file(s) /app/software/GCC/6.4.0-2.28/easybuild/easybuild-GCC-6.4.0-20180424.084946.log
== Build succeeded for 15 out of 15
...
Building Singularity image...
Singularity container built: /home/example/.local/easybuild/containers/GCC-6.4.0-2.28.simg
Cleaning up...
== Singularity image created at /home/example/.local/easybuild/containers/GCC-6.4.0-2.28.simg
== Temporary log file(s) /tmp/eb-aYXYC8/easybuild-8uXhvu.log* have been removed.
== Temporary directory /tmp/eb-aYXYC8 has been removed.

The inspect the container image, you can use singularity shell to start a shell session in the container:

$ singularity shell --shell "/bin/bash --norc" $HOME/.local/easybuild/containers/GCC-6.4.0-2.28.simg

Singularity GCC-6.4.0-2.28.simg:~> source /etc/profile

Singularity GCC-6.4.0-2.28.simg:~> module list

Currently Loaded Modules:
  1) GCCcore/6.4.0   2) binutils/2.28-GCCcore-6.4.0   3) GCC/6.4.0-2.28

Singularity GCC-6.4.0-2.28.simg:~> which gcc
/app/software/GCCcore/6.4.0/bin/gcc

Singularity GCC-6.4.0-2.28.simg:~> gcc --version
gcc (GCC) 6.4.0
...

Note

We are passing --shell "/bin/bash --norc to singularity shell to avoid that the .bashrc login script thay may be present in your home directory is sourced, since that may include statements that are not relevant in the container environment.

Note

The source /etc/profile statement should not be required, we intend to fix this in future updates.

Or, you can use singularity exec to execute a command in the container.

Compare the output of running which gcc and gcc --version locally:

$ which gcc
/usr/bin/gcc
$ gcc --version
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-16)
...

and the output when running the same commands in the container:

$ singularity exec GCC-6.4.0-2.28.simg which gcc
/app/software/GCCcore/6.4.0/bin/gcc

$ singularity exec GCC-6.4.0-2.28.simg gcc --version
gcc (GCC) 6.4.0
...

Configuration

Note

You can specify each of these configuration options either as options to the eb command, via the equivalent $EASYBUILD_CONTAINER* environment variable, or via an EasyBuild configuation file; see Supported configuration types.

Location for generated container recipes & images (--containerpath)

To control the location where EasyBuild will put generated container recipes & images, use the --containerpath configuration setting. Next to providing this as an option to the eb command, you can also define the $EASYBUILD_CONTAINERPATH environment variable or specify containerpath in an EasyBuild configuration file.

The default value for this location is $HOME/.local/easybuild/containers, unless the --prefix configuration setting was provided, in which case it becomes <prefix>/containers (see Overall prefix path (--prefix)).

Use eb --show-full-config | grep containerpath to determine the currently active setting.

Container image format (--container-image-format)

The format for container images that EasyBuild is produces via the functionality provided by the container software can be controlled via the --container-image-format configuration setting.

For Singularity containers (see Type of container recipe/image to generate (--container-type)), three image formats are supported:

  • squashfs (default): compressed images using squashfs read-only file system
  • ext3: writable image file using ext3 file system
  • sandbox: container image in a regular directory

See also https://singularity.lbl.gov/user-guide#supported-container-formats and http://singularity.lbl.gov/docs-build-container.

Name for container recipe & image (--container-image-name)

By default, EasyBuild will use the name of the first easyconfig file (without the .eb suffix) as a name for both the container recipe and image.

You can specify an altername name using the --container-image-name configuration setting.

The filename of generated container recipe will be Singularity.<name>.

The filename of the container image will be <name><extension>, where the value for <extension> depends on the image format (see Container image format (--container-image-format)):

  • .simg’ for squashfs container images
  • .img’ for ext3 container images
  • empty for sandbox container images (in which case the container image is actually a directory rather than a file)

Temporary directory for creating container images (--container-tmpdir)

The container software that EasyBuild leverages to build container images may be using a temporary directory in a location that doesn’t have sufficient free space.

You can instruct EasyBuild to pass an alternate location via the --container-tmpdir configuration setting.

For Singularity, the default is to use /tmp, see http://singularity.lbl.gov/build-environment#temporary-folders. If --container-tmpdir is specified, the $SINGULARITY_TMPDIR environment variable will be defined accordingly to let Singularity use that location instead.

Type of container recipe/image to generate (--container-type)

With the --container-type configuration option, you can specify what type of container recipe/image EasyBuild should generated. Possible values are:

Note

Currently (since EasyBuild v3.6.0) only singularity is actually supported.

‘Stacking’ container images

To avoid long build times and excessive large container images, you can construct your target container image step-by-step, by first building a base container image for the compiler toolchain you want to use, and then using it to build a container images for a particular (set of) software package(s).

For example, to build a container image for Python 3.6.4 built with the foss/2018a toolchain:

$ cd /tmp

# use current directory as location for generated container recipes & images
$ export EASYBUILD_CONTAINERPATH=$PWD

# build base container image for OpenMPI + GCC parts of foss/2018a toolchain, on top of CentOS 7.4 base image from Singularity Hub
$ eb -C --container-build-image OpenMPI-2.1.2-GCC-6.4.0-2.28.eb --container-base shub:shahzebsiddiqui/eb-singularity:centos-7.4.1708 --experimental
...
== Singularity image created at /tmp/OpenMPI-2.1.2-GCC-6.4.0-2.28.simg
...

$ ls -lh OpenMPI-2.1.2-GCC-6.4.0-2.28.simg
-rwxr-xr-x 1 root root 590M Apr 24 11:43 OpenMPI-2.1.2-GCC-6.4.0-2.28.simg

# build another container image for the for the full foss/2018a toolchain, using the OpenMPI + GCC container as a base
$ eb -C --container-build-image foss-2018a.eb --container-base localimage:$PWD/OpenMPI-2.1.2-GCC-6.4.0-2.28.simg --experimental
...
== Singularity image created at /tmp/foss-2018a.simg
...

$ ls -lh foss-2018a.simg
-rwxr-xr-x 1 root root 614M Apr 24 13:11 foss-2018a.simg

# build container image for Python 3.6.4 with foss/2018a toolchain by leveraging base container image foss-2018a.simg
$ eb -C --container-build-image Python-3.6.4-foss-2018a.eb --container-base localimage:$PWD/foss-2018a.simg --experimental
...
== Singularity image created at /tmp/Python-3.6.4-foss-2018a.simg
...

$ ls -lh Python-3.6.4-foss-2018a.simg
-rwxr-xr-x 1 root root 759M Apr 24 14:01 Python-3.6.4-foss-2018a.simg

$ singularity exec Python-3.6.4-foss-2018a.simg which python
/app/software/Python/3.6.4-foss-2018a/bin/python

$ singularity exec Python-3.6.4-foss-2018a.simg python -V
vsc40023 belongs to gsingularity
Python 3.6.4