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