c9ba95cc5c
Before this fix, `spack containerize` complains that `centos/7` is invalid (should have been `centos:7`)
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ReStructuredText
.. Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
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Spack Project Developers. See the top-level COPYRIGHT file for details.
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SPDX-License-Identifier: (Apache-2.0 OR MIT)
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.. _containers:
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================
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Container Images
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================
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Spack :ref:`environments` are a great tool to create container images, but
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preparing one that is suitable for production requires some more boilerplate
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than just:
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.. code-block:: docker
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COPY spack.yaml /environment
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RUN spack -e /environment install
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Additional actions may be needed to minimize the size of the
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container, or to update the system software that is installed in the base
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image, or to set up a proper entrypoint to run the image. These tasks are
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usually both necessary and repetitive, so Spack comes with a command
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to generate recipes for container images starting from a ``spack.yaml``.
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--------------------
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A Quick Introduction
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--------------------
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Consider having a Spack environment like the following:
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.. code-block:: yaml
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spack:
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specs:
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- gromacs+mpi
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- mpich
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Producing a ``Dockerfile`` from it is as simple as moving to the directory
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where the ``spack.yaml`` file is stored and giving the following command:
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.. code-block:: console
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$ spack containerize > Dockerfile
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The ``Dockerfile`` that gets created uses multi-stage builds and
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other techniques to minimize the size of the final image:
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.. code-block:: docker
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# Build stage with Spack pre-installed and ready to be used
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FROM spack/ubuntu-bionic:latest as builder
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# What we want to install and how we want to install it
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# is specified in a manifest file (spack.yaml)
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RUN mkdir /opt/spack-environment \
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&& (echo "spack:" \
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&& echo " specs:" \
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&& echo " - gromacs+mpi" \
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&& echo " - mpich" \
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&& echo " concretization: together" \
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&& echo " config:" \
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&& echo " install_tree: /opt/software" \
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&& echo " view: /opt/view") > /opt/spack-environment/spack.yaml
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# Install the software, remove unnecessary deps
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RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
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# Strip all the binaries
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RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
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xargs file -i | \
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grep 'charset=binary' | \
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grep 'x-executable\|x-archive\|x-sharedlib' | \
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awk -F: '{print $1}' | xargs strip -s
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# Modifications to the environment that are necessary to run
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RUN cd /opt/spack-environment && \
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spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
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# Bare OS image to run the installed executables
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FROM ubuntu:18.04
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COPY --from=builder /opt/spack-environment /opt/spack-environment
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COPY --from=builder /opt/software /opt/software
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COPY --from=builder /opt/view /opt/view
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COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
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ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
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The image itself can then be built and run in the usual way, with any of the
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tools suitable for the task. For instance, if we decided to use ``docker``:
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.. code-block:: bash
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$ spack containerize > Dockerfile
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$ docker build -t myimage .
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[ ... ]
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$ docker run -it myimage
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The various components involved in the generation of the recipe and their
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configuration are discussed in details in the sections below.
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.. _container_spack_images:
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--------------------------
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Spack Images on Docker Hub
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--------------------------
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Docker images with Spack preinstalled and ready to be used are
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built on `Docker Hub <https://hub.docker.com/u/spack>`_
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at every push to ``develop`` or to a release branch. The OS that
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are currently supported are summarized in the table below:
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.. _containers-supported-os:
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.. list-table:: Supported operating systems
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:header-rows: 1
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* - Operating System
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- Base Image
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- Spack Image
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* - Ubuntu 16.04
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- ``ubuntu:16.04``
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- ``spack/ubuntu-xenial``
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* - Ubuntu 18.04
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- ``ubuntu:18.04``
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- ``spack/ubuntu-bionic``
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* - CentOS 6
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- ``centos:6``
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- ``spack/centos6``
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* - CentOS 7
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- ``centos:7``
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- ``spack/centos7``
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All the images are tagged with the corresponding release of Spack:
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.. image:: dockerhub_spack.png
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with the exception of the ``latest`` tag that points to the HEAD
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of the ``develop`` branch. These images are available for anyone
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to use and take care of all the repetitive tasks that are necessary
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to setup Spack within a container. The container recipes generated
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by Spack use them as default base images for their ``build`` stage,
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even though handles to use custom base images provided by users are
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available to accommodate complex use cases.
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---------------------------------
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Creating Images From Environments
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---------------------------------
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Any Spack Environment can be used for the automatic generation of container
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recipes. Sensible defaults are provided for things like the base image or the
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version of Spack used in the image.
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If a finer tuning is needed it can be obtained by adding the relevant metadata
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under the ``container`` attribute of environments:
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.. code-block:: yaml
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spack:
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specs:
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- gromacs+mpi
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- mpich
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container:
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# Select the format of the recipe e.g. docker,
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# singularity or anything else that is currently supported
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format: docker
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# Sets the base images for the stages where Spack builds the
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# software or where the software gets installed after being built..
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images:
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os: "centos:7"
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spack: develop
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# Whether or not to strip binaries
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strip: true
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# Additional system packages that are needed at runtime
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os_packages:
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final:
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- libgomp
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# Extra instructions
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extra_instructions:
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final: |
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RUN echo 'export PS1="\[$(tput bold)\]\[$(tput setaf 1)\][gromacs]\[$(tput setaf 2)\]\u\[$(tput sgr0)\]:\w $ "' >> ~/.bashrc
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# Labels for the image
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labels:
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app: "gromacs"
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mpi: "mpich"
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A detailed description of the options available can be found in the
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:ref:`container_config_options` section.
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-------------------
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Setting Base Images
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-------------------
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The ``images`` subsection is used to select both the image where
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Spack builds the software and the image where the built software
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is installed. This attribute can be set in two different ways and
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which one to use depends on the use case at hand.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Use Official Spack Images From Dockerhub
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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To generate a recipe that uses an official Docker image from the
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Spack organization to build the software and the corresponding official OS image
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to install the built software, all the user has to do is specify:
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1. An operating system under ``images:os``
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2. A Spack version under ``images:spack``
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Any combination of these two values that can be mapped to one of the images
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discussed in :ref:`container_spack_images` is allowed. For instance, the
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following ``spack.yaml``:
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.. code-block:: yaml
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spack:
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specs:
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- gromacs+mpi
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- mpich
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container:
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images:
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os: centos:7
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spack: 0.15.4
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uses ``spack/centos7:0.15.4`` and ``centos:7`` for the stages where the
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software is respectively built and installed:
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.. code-block:: docker
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# Build stage with Spack pre-installed and ready to be used
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FROM spack/centos7:0.15.4 as builder
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# What we want to install and how we want to install it
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# is specified in a manifest file (spack.yaml)
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RUN mkdir /opt/spack-environment \
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&& (echo "spack:" \
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&& echo " specs:" \
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&& echo " - gromacs+mpi" \
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&& echo " - mpich" \
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&& echo " concretization: together" \
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&& echo " config:" \
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&& echo " install_tree: /opt/software" \
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&& echo " view: /opt/view") > /opt/spack-environment/spack.yaml
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[ ... ]
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# Bare OS image to run the installed executables
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FROM centos:7
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COPY --from=builder /opt/spack-environment /opt/spack-environment
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COPY --from=builder /opt/software /opt/software
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COPY --from=builder /opt/view /opt/view
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COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
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ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
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This method of selecting base images is the simplest of the two, and we advise
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to use it whenever possible. There are cases though where using Spack official
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images is not enough to fit production needs. In these situations users can manually
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select which base image to start from in the recipe, as we'll see next.
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Use Custom Images Provided by Users
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^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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Consider, as an example, building a production grade image for a CUDA
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application. The best strategy would probably be to build on top of
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images provided by the vendor and regard CUDA as an external package.
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Spack doesn't currently provide an official image with CUDA configured
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this way, but users can build it on their own and then configure the
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environment to explicitly pull it. This requires users to:
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1. Specify the image used to build the software under ``images:build``
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2. Specify the image used to install the built software under ``images:final``
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A ``spack.yaml`` like the following:
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.. code-block:: yaml
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spack:
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specs:
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- gromacs@2019.4+cuda build_type=Release
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- mpich
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- fftw precision=float
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packages:
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cuda:
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buildable: False
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externals:
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- spec: cuda%gcc
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prefix: /usr/local/cuda
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container:
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images:
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build: custom/cuda-10.1-ubuntu18.04:latest
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final: nvidia/cuda:10.1-base-ubuntu18.04
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produces, for instance, the following ``Dockerfile``:
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.. code-block:: docker
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# Build stage with Spack pre-installed and ready to be used
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FROM custom/cuda-10.1-ubuntu18.04:latest as builder
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# What we want to install and how we want to install it
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# is specified in a manifest file (spack.yaml)
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RUN mkdir /opt/spack-environment \
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&& (echo "spack:" \
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&& echo " specs:" \
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&& echo " - gromacs@2019.4+cuda build_type=Release" \
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&& echo " - mpich" \
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&& echo " - fftw precision=float" \
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&& echo " packages:" \
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&& echo " cuda:" \
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&& echo " buildable: false" \
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&& echo " externals:" \
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&& echo " - spec: cuda%gcc" \
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&& echo " prefix: /usr/local/cuda" \
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&& echo " concretization: together" \
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&& echo " config:" \
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&& echo " install_tree: /opt/software" \
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&& echo " view: /opt/view") > /opt/spack-environment/spack.yaml
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# Install the software, remove unnecessary deps
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RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
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# Strip all the binaries
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RUN find -L /opt/view/* -type f -exec readlink -f '{}' \; | \
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xargs file -i | \
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grep 'charset=binary' | \
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grep 'x-executable\|x-archive\|x-sharedlib' | \
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awk -F: '{print $1}' | xargs strip -s
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# Modifications to the environment that are necessary to run
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RUN cd /opt/spack-environment && \
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spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
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# Bare OS image to run the installed executables
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FROM nvidia/cuda:10.1-base-ubuntu18.04
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COPY --from=builder /opt/spack-environment /opt/spack-environment
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COPY --from=builder /opt/software /opt/software
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COPY --from=builder /opt/view /opt/view
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COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
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ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
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where the base images for both stages are completely custom.
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This second mode of selection for base images is more flexible than just
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choosing an operating system and a Spack version, but is also more demanding.
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Users may need to generate by themselves their base images and it's also their
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responsibility to ensure that:
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1. Spack is available in the ``build`` stage and set up correctly to install the required software
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2. The artifacts produced in the ``build`` stage can be executed in the ``final`` stage
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Therefore we don't recommend its use in cases that can be otherwise
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covered by the simplified mode shown first.
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----------------------------
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Singularity Definition Files
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----------------------------
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In addition to producing recipes in ``Dockerfile`` format Spack can produce
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Singularity Definition Files by just changing the value of the ``format``
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attribute:
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.. code-block:: console
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$ cat spack.yaml
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spack:
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specs:
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- hdf5~mpi
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container:
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format: singularity
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$ spack containerize > hdf5.def
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$ sudo singularity build hdf5.sif hdf5.def
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The minimum version of Singularity required to build a SIF (Singularity Image Format)
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image from the recipes generated by Spack is ``3.5.3``.
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.. _container_config_options:
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-----------------------
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Configuration Reference
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-----------------------
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The tables below describe all the configuration options that are currently supported
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to customize the generation of container recipes:
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.. list-table:: General configuration options for the ``container`` section of ``spack.yaml``
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:header-rows: 1
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* - Option Name
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- Description
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- Allowed Values
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- Required
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* - ``format``
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- The format of the recipe
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- ``docker`` or ``singularity``
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- Yes
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* - ``images:os``
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- Operating system used as a base for the image
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- See :ref:`containers-supported-os`
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- Yes, if using constrained selection of base images
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* - ``images:spack``
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- Version of Spack use in the ``build`` stage
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- Valid tags for ``base:image``
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- Yes, if using constrained selection of base images
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* - ``images:build``
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- Image to be used in the ``build`` stage
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- Any valid container image
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- Yes, if using custom selection of base images
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* - ``images:final``
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- Image to be used in the ``build`` stage
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- Any valid container image
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- Yes, if using custom selection of base images
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* - ``strip``
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- Whether to strip binaries
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- ``true`` (default) or ``false``
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- No
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* - ``os_packages:command``
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- Tool used to manage system packages
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- ``apt``, ``yum``
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- Only with custom base images
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* - ``os_packages:update``
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- Whether or not to update the list of available packages
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- True or False (default: True)
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- No
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* - ``os_packages:build``
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- System packages needed at build-time
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- Valid packages for the current OS
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- No
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* - ``os_packages:final``
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- System packages needed at run-time
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- Valid packages for the current OS
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- No
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* - ``extra_instructions:build``
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- Extra instructions (e.g. `RUN`, `COPY`, etc.) at the end of the ``build`` stage
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- Anything understood by the current ``format``
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- No
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* - ``extra_instructions:final``
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- Extra instructions (e.g. `RUN`, `COPY`, etc.) at the end of the ``final`` stage
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- Anything understood by the current ``format``
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- No
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* - ``labels``
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- Labels to tag the image
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- Pairs of key-value strings
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- No
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.. list-table:: Configuration options specific to Singularity
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:header-rows: 1
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* - Option Name
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- Description
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- Allowed Values
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- Required
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* - ``singularity:runscript``
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- Content of ``%runscript``
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- Any valid script
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- No
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* - ``singularity:startscript``
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- Content of ``%startscript``
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- Any valid script
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- No
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* - ``singularity:test``
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- Content of ``%test``
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- Any valid script
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- No
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* - ``singularity:help``
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- Description of the image
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- Description string
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- No
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--------------
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Best Practices
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--------------
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^^^
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MPI
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^^^
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Due to the dependency on Fortran for OpenMPI, which is the spack default
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implementation, consider adding ``gfortran`` to the ``apt-get install`` list.
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Recent versions of OpenMPI will require you to pass ``--allow-run-as-root``
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to your ``mpirun`` calls if started as root user inside Docker.
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For execution on HPC clusters, it can be helpful to import the docker
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image into Singularity in order to start a program with an *external*
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MPI. Otherwise, also add ``openssh-server`` to the ``apt-get install`` list.
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^^^^
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CUDA
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^^^^
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Starting from CUDA 9.0, Nvidia provides minimal CUDA images based on
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Ubuntu. Please see `their instructions <https://hub.docker.com/r/nvidia/cuda/>`_.
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Avoid double-installing CUDA by adding, e.g.
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.. code-block:: yaml
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packages:
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cuda:
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externals:
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- spec: "cuda@9.0.176%gcc@5.4.0 arch=linux-ubuntu16-x86_64"
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prefix: /usr/local/cuda
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buildable: False
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to your ``spack.yaml``.
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Users will either need ``nvidia-docker`` or e.g. Singularity to *execute*
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device kernels.
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^^^^^^^^^^^^^^^^^^^^^^^^^
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Docker on Windows and OSX
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^^^^^^^^^^^^^^^^^^^^^^^^^
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On Mac OS and Windows, docker runs on a hypervisor that is not allocated much
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memory by default, and some spack packages may fail to build due to lack of
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memory. To work around this issue, consider configuring your docker installation
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to use more of your host memory. In some cases, you can also ease the memory
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pressure on parallel builds by limiting the parallelism in your config.yaml.
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.. code-block:: yaml
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config:
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build_jobs: 2
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