`spack containerize` generates containers from envs (#14202)

This PR adds a new command to Spack:
```console
$ spack containerize -h
usage: spack containerize [-h] [--config CONFIG]

creates recipes to build images for different container runtimes

optional arguments:
  -h, --help       show this help message and exit
  --config CONFIG  configuration for the container recipe that will be generated
```
which takes an environment with an additional `container` section:
```yaml
spack:
  specs:
  - gromacs build_type=Release 
  - mpich
  - fftw precision=float
  packages:
    all:
      target: [broadwell]

  container:
    # Select the format of the recipe e.g. docker,
    # singularity or anything else that is currently supported
    format: docker
    
    # Select from a valid list of images
    base:
      image: "ubuntu:18.04"
      spack: prerelease

    # Additional system packages that are needed at runtime
    os_packages:
    - libgomp1
```
and turns it into a `Dockerfile` or a Singularity definition file, for instance:
```Dockerfile
# Build stage with Spack pre-installed and ready to be used
FROM spack/ubuntu-bionic:prerelease 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 build_type=Release" \
&&   echo "  - mpich" \
&&   echo "  - fftw precision=float" \
&&   echo "  packages:" \
&&   echo "    all:" \
&&   echo "      target:" \
&&   echo "      - broadwell" \
&&   echo "  config:" \
&&   echo "    install_tree: /opt/software" \
&&   echo "  concretization: together" \
&&   echo "  view: /opt/view") > /opt/spack-environment/spack.yaml

# Install the software, remove unecessary deps and strip executables
RUN cd /opt/spack-environment && spack install && spack autoremove -y
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

RUN apt-get -yqq update && apt-get -yqq upgrade                                   \
 && apt-get -yqq install libgomp1 \
 && rm -rf /var/lib/apt/lists/*

ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
```

3 files changed, 146 insertions, 1 deletions

diff --git a/share/spack/spack-completion.bash b/share/spack/spack-completion.bash
index b408d0b234..623e9fba73 100755
--- a/share/spack/spack-completion.bash
+++ b/share/spack/spack-completion.bash
@@ -313,7 +313,7 @@ _spack() {
     then
         SPACK_COMPREPLY="-h --help -H --all-help --color -C --config-scope -d --debug --timestamp --pdb -e --env -D --env-dir -E --no-env --use-env-repo -k --insecure -l --enable-locks -L --disable-locks -m --mock -p --profile --sorted-profile --lines -v --verbose --stacktrace -V --version --print-shell-vars"
     else
-        SPACK_COMPREPLY="activate add arch blame bootstrap build build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config configure create deactivate debug dependencies dependents deprecate dev-build diy docs edit env extensions fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload upload-s3 url verify versions view"
+        SPACK_COMPREPLY="activate add arch blame bootstrap build build-env buildcache cd checksum ci clean clone commands compiler compilers concretize config configure containerize create deactivate debug dependencies dependents deprecate dev-build diy docs edit env extensions fetch find flake8 gc gpg graph help info install license list load location log-parse maintainers mirror module patch pkg providers pydoc python reindex remove rm repo resource restage setup spec stage test uninstall unload upload-s3 url verify versions view"
     fi
 }
 
@@ -628,6 +628,10 @@ _spack_configure() {
     fi
 }
 
+_spack_containerize() {
+    SPACK_COMPREPLY="-h --help"
+}
+
 _spack_create() {
     if $list_options
     then
diff --git a/share/spack/templates/container/Dockerfile b/share/spack/templates/container/Dockerfile
new file mode 100644
index 0000000000..740f46e9ee
--- /dev/null
+++ b/share/spack/templates/container/Dockerfile
@@ -0,0 +1,51 @@
+# Build stage with Spack pre-installed and ready to be used
+FROM {{ build.image }}:{{ build.tag }} as builder
+
+# What we want to install and how we want to install it
+# is specified in a manifest file (spack.yaml)
+RUN mkdir {{ paths.environment }} \
+{{ manifest }} > {{ paths.environment }}/spack.yaml
+
+# Install the software, remove unecessary deps
+RUN cd {{ paths.environment }} && spack install && spack gc -y
+{% if strip %}
+
+# Strip all the binaries
+RUN find -L {{ paths.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
+{% endif %}
+
+# Modifications to the environment that are necessary to run
+RUN cd {{ paths.environment }} && \
+    spack env activate --sh -d . >> /etc/profile.d/z10_spack_environment.sh
+
+{% if extra_instructions.build %}
+{{ extra_instructions.build }}
+{% endif %}
+
+# Bare OS image to run the installed executables
+FROM {{ run.image }}
+
+COPY --from=builder {{ paths.environment }} {{ paths.environment }}
+COPY --from=builder {{ paths.store }} {{ paths.store }}
+COPY --from=builder {{ paths.view }} {{ paths.view }}
+COPY --from=builder /etc/profile.d/z10_spack_environment.sh /etc/profile.d/z10_spack_environment.sh
+
+{% if os_packages %}
+RUN {{ os_packages.update }}                                   \
+ && {{ os_packages.install }}{% for pkg in os_packages.list %} {{ pkg }}{% endfor %} \
+ && {{ os_packages.clean }}
+{% endif %}
+
+{% if extra_instructions.final %}
+{{ extra_instructions.final }}
+{% endif %}
+
+{% for label, value in labels.items() %}
+LABEL "{{ label }}"="{{ value }}"
+{% endfor %}
+
+ENTRYPOINT ["/bin/bash", "--rcfile", "/etc/profile", "-l"]
diff --git a/share/spack/templates/container/singularity.def b/share/spack/templates/container/singularity.def
new file mode 100644
index 0000000000..616e677f96
--- /dev/null
+++ b/share/spack/templates/container/singularity.def
@@ -0,0 +1,90 @@
+Bootstrap: docker
+From: {{ build.image }}:{{ build.tag }}
+Stage: build
+
+%post
+  # Create the manifest file for the installation in /opt/spack-environment
+  mkdir {{ paths.environment }} && cd {{ paths.environment }}
+  cat << EOF > spack.yaml
+{{ manifest }}
+EOF
+
+  # Install all the required software
+  . /opt/spack/share/spack/setup-env.sh
+  spack install
+  spack gc -y
+  spack env activate --sh -d . >> {{ paths.environment }}/environment_modifications.sh
+{% if strip %}
+
+  # Strip the binaries to reduce the size of the image
+  find -L {{ paths.view }}/* -type f -exec readlink -f '{}' \; | \
+    xargs file -i | \
+    grep 'charset=binary' | \
+    grep 'x-executable\|x-archive\|x-sharedlib' | \
+    awk -F: '{print $1}' | xargs strip -s
+{% endif %}
+{% if extra_instructions.build %}
+{{ extra_instructions.build }}
+{% endif %}
+
+
+{% if apps %}
+{% for application, help_text in apps.items() %}
+
+%apprun {{ application }}
+    exec /opt/view/bin/{{ application }} "$@"
+
+%apphelp {{ application }}
+    {{help_text }}
+{% endfor %}
+{% endif %}
+
+Bootstrap: docker
+From: {{ run.image }}
+Stage: final
+
+%files from build
+  {{ paths.environment }} /opt
+  {{ paths.store }} /opt
+  {{ paths.view }} /opt
+  {{ paths.environment }}/environment_modifications.sh {{ paths.environment }}/environment_modifications.sh
+
+%post
+{% if os_packages.list %}
+  # Update, install and cleanup of system packages
+  {{ os_packages.update }}
+  {{ os_packages.install }} {{ os_packages.list | join | replace('\n', ' ') }}
+  {{ os_packages.clean }}
+{% endif %}
+  # Modify the environment without relying on sourcing shell specific files at startup
+  cat {{ paths.environment }}/environment_modifications.sh >> $SINGULARITY_ENVIRONMENT
+{% if extra_instructions.final %}
+{{ extra_instructions.final }}
+{% endif %}
+
+{% if runscript %}
+%runscript
+{{ runscript }}
+{% endif %}
+
+{% if startscript %}
+%startscript
+{{ startscript }}
+{% endif %}
+
+{% if test %}
+%test
+{{ test }}
+{% endif %}
+
+{% if help %}
+%help
+{{ help }}
+{% endif %}
+
+{% if labels %}
+%labels
+{% for label, value in labels.items() %}
+  {{ label }} {{ value }}
+{% endfor %}
+{% endif %}
\ No newline at end of file