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author | Massimiliano Culpo <massimiliano.culpo@gmail.com> | 2020-01-31 02:19:55 +0100 |
---|---|---|
committer | GitHub <noreply@github.com> | 2020-01-30 17:19:55 -0800 |
commit | 9635ff3d20c17a92a89cf82db8d3f877dd04e1c7 (patch) | |
tree | fb4e5d0b2319a308e24572fa06e7399cbad88bf2 /share/spack/templates | |
parent | ed501eaab275f50dc3d689ee9e8d6c7fa707fd94 (diff) | |
download | spack-9635ff3d20c17a92a89cf82db8d3f877dd04e1c7.tar.gz spack-9635ff3d20c17a92a89cf82db8d3f877dd04e1c7.tar.bz2 spack-9635ff3d20c17a92a89cf82db8d3f877dd04e1c7.tar.xz spack-9635ff3d20c17a92a89cf82db8d3f877dd04e1c7.zip |
`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"]
```
Diffstat (limited to 'share/spack/templates')
-rw-r--r-- | share/spack/templates/container/Dockerfile | 51 | ||||
-rw-r--r-- | share/spack/templates/container/singularity.def | 90 |
2 files changed, 141 insertions, 0 deletions
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 |