Merge branch 'develop' into features/shared

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
 }
 
@@ -400,7 +400,7 @@ _spack_buildcache_install() {
 _spack_buildcache_list() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -l --long -L --very-long -v --variants -f --force"
+        SPACK_COMPREPLY="-h --help -l --long -L --very-long -v --variants -f --force -a --allarch"
     else
         _all_packages
     fi
@@ -628,6 +628,10 @@ _spack_configure() {
     fi
 }
 
+_spack_containerize() {
+    SPACK_COMPREPLY="-h --help"
+}
+
 _spack_create() {
     if $list_options
     then
@@ -941,7 +945,7 @@ _spack_info() {
 _spack_install() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help --only -u --until -j --jobs --overwrite --keep-prefix --keep-stage --dont-restage --use-cache --no-cache --cache-only --show-log-on-error --source -n --no-checksum -v --verbose --fake --only-concrete -f --file --upstream -g --global --clean --dirty --test --run-tests --log-format --log-file --help-cdash --cdash-upload-url --cdash-build --cdash-site --cdash-track --cdash-buildstamp -y --yes-to-all"
+        SPACK_COMPREPLY="-h --help --only -u --until -j --jobs --overwrite --keep-prefix --keep-stage --dont-restage --use-cache --no-cache --cache-only --no-check-signature --show-log-on-error --source -n --no-checksum -v --verbose --fake --only-concrete -f --file --clean --dirty --test --run-tests --log-format --log-file --help-cdash --cdash-upload-url --cdash-build --cdash-site --cdash-track --cdash-buildstamp -y --yes-to-all"
     else
         _all_packages
     fi
@@ -1415,7 +1419,7 @@ _spack_test() {
 _spack_uninstall() {
     if $list_options
     then
-        SPACK_COMPREPLY="-h --help -f --force -R --dependents -y --yes-to-all -a --all -u --upstream -g --global"
+        SPACK_COMPREPLY="-h --help -f --force -R --dependents -y --yes-to-all -a --all"
     else
         _installed_packages
     fi
@@ -1592,4 +1596,4 @@ _spack_view_check() {
     else
         _all_packages
     fi
-}
+}

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"]

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 %}