add spack config yaml and template to generate dockerfile

Dockerfile

@@ -17,35 +17,75 @@
 # License along with FRE-NCTools.  If not, see
 # <http://www.gnu.org/licenses/>.
 #***********************************************************************
+# Build stage with Spack pre-installed and ready to be used
+FROM spack/rockylinux9: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 '  - gcc' \
+&&   echo '  - mpich' \
+&&   echo '  - netcdf-c' \
+&&   echo '  - netcdf-fortran' \
+&&   echo '  - nccmp' \
+&&   echo '  concretizer:' \
+&&   echo '    unify: true' \
+&&   echo '  packages:' \
+&&   echo '    all:' \
+&&   echo '      compiler: [gcc]' \
+&&   echo '  config:' \
+&&   echo '    template_dirs:' \
+&&   echo '    - /home/rem/fre-nctools-container/template' \
+&&   echo '  # container specific options' \
+&&   echo '    install_tree: /opt/software' \
+&&   echo '  view: /opt/views/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
+
+# Modifications to the environment that are necessary to run
+RUN cd /opt/spack-environment && \
+    spack env activate --sh -d . > activate.sh
+
+
+
+# Bare OS image to run the installed executables
+FROM docker.io/rockylinux:9
+
+COPY --from=builder /opt/spack-environment /opt/spack-environment
+COPY --from=builder /opt/software /opt/software
+
+# paths.view is a symlink, so copy the parent to avoid dereferencing and duplicating it
+COPY --from=builder /opt/views /opt/views
+
+RUN { \
+      echo '#!/bin/sh' \
+      && echo '.' /opt/spack-environment/activate.sh \
+      && echo 'exec "$@"'; \
+    } > /entrypoint.sh \
+&& chmod a+x /entrypoint.sh \
+&& ln -s /opt/views/view /opt/view
+
+
+RUN dnf update -y && dnf install -y epel-release && dnf update -y \
+ && dnf install -y autoconf libtool make bats git libgomp python3 python3-numpy python3-pip python3-pytest \
+ && rm -rf /var/cache/dnf && dnf clean all
+
+# Install any needed pip packages
+RUN pip install git+https://github.com/adcroft/numpypi.git && \
+    pip install netCDF4 virtualenv
+# Set compilers for mpich wrappers
+ENV MPICH_FC=gfortran
+ENV MPICH_CC=gcc
+LABEL "maintainer"="Seth Underwood <[email protected]>"
+LABEL "copyright"="2021, 2022, 2023 GFDL"
+LABEL "license"="LGPL v3+"
+LABEL "gov.noaa.gfdl.version"="5.0.0"
+LABEL "vendor"="Geophysical Fluid Dynamics Laboratory"
+LABEL "gov.noaa.gfdl.release-date"="2024-01-07"
+ENTRYPOINT [ "/entrypoint.sh" ]
+CMD [ "/bin/bash" ]
 
-FROM ubuntu:focal
-LABEL maintainer="Seth Underwood <[email protected]>"
-LABEL copyright="2021, 2022 GFDL"
-LABEL license="LGPL v3+"
-LABEL gov.noaa.gfdl.version="3.0.0"
-LABEL vendor="Geophysical Fluid Dynamics Laboratory"
-LABEL gov.noaa.gfdl.release-date="2022-02-20"
-
-## install fre-nctools dependencies
-RUN apt-get update \
- && apt-get -y install software-properties-common \
- && add-apt-repository ppa:underwoo/nccmp --update \
- && apt-get install -y \
-    autoconf \
-    bats \
-    gfortran \
-    git \
-    libnetcdf-dev \
-    libnetcdff-dev \
-    make \
-    nccmp \
-    netcdf-bin \
-    python \
-    python3-netcdf4 \
-    python3-numpy \
-    python3-pip \
-    python3-pytest \
-    python3-venv \
-    mpich \
-    libmpich-dev \
- && pip install git+https://github.com/adcroft/numpypi.git

README.md

@@ -1,10 +1,16 @@
 # FRE-NCtools-container
 
-Recipefile and associated container used for the CI testing of the 
+Spack config and generated Dockerfile for container used for the CI testing of the
 [FRE-NCtools repository](github.com/NOAA-GFDL/FRE-NCtools). Container is based
-on Ubuntu Focal and includes all the required libraries for building and running
+on Rocky Linux 9 and includes all the required libraries for building and running
 the FRE-NCtools test suite.
 
+The Dockerfile is meant to be auto-generated with `spack containerize` via the provided
+yaml and template files. Instructions to do so are provided in `spack.yaml`.
+
+Any modifications should be made to these files, `spack.yaml` and `template/Dockerfile.template`
+instead of the resulting Dockerfile (which should then be generated and added accordingly).
+
 # Support
 
 At this time, the container(s) in this repository are used for internal testing

spack.yaml

@@ -0,0 +1,80 @@
+#***********************************************************************
+#                   GNU Lesser General Public License
+#
+# This file is part of the GFDL FRE NetCDF tools package (FRE-NCTools).
+#
+# FRE-NCTools is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at
+# your option) any later version.
+#
+# FRE-NCTools is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+# for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with FRE-NCTools.  If not, see
+# <http://www.gnu.org/licenses/>.
+#***********************************************************************
+# Ryan Mulhall 2023
+# spack environment config to generate a dockerfile for the fre-nctools ci image.
+# After any updates to generate a new dockerfile you must fill in the template_dirs below with your current
+# directory and run the following:
+#
+#     <clone spack and source spack/share/spack/setup-env.sh)
+#     spack env create fnct-container-env spack.yaml
+#     spack env activate fnct-container-env
+#     spack containerize > Dockerfile
+#
+# For versions, spack packages will use the default (usually the newest but depends on whats compatible)
+# Images should be tagged with gcc version used
+spack:
+  specs:
+  - gcc
+  - mpich
+  - netcdf-c
+  - netcdf-fortran
+  - nccmp
+  concretizer:
+    unify: true
+  packages:
+    all:
+      compiler: [ gcc ]
+  config:
+    template_dirs:
+      - /home/rem/fre-nctools-container/template
+  # container specific options
+  container:
+    format: docker
+    template: Dockerfile.template
+    images:
+      os: "rockylinux:9"
+      spack: develop
+    # labels for final image
+    labels:
+      maintainer: "Seth Underwood <[email protected]>"
+      copyright: "2021, 2022, 2023 GFDL"
+      license: "LGPL v3+"
+      gov.noaa.gfdl.version: "5.0.0"
+      vendor: "Geophysical Fluid Dynamics Laboratory"
+      gov.noaa.gfdl.release-date: "2024-01-10"
+    # TODO should strip binaries for size if possible
+    # currently causes linker issues with libgcc when true
+    strip: false
+    # Additional packages that are needed at (ci) runtime
+    # this is anything that doesn't need to be built from source
+    # pip installs would be added in the template instead
+    os_packages:
+      final:
+      - autoconf
+      - libtool
+      - make
+      - bats
+      - git
+      - libgomp
+      - python3
+      - python3-numpy
+      - python3-pip
+      - python3-pytest
+

template/Dockerfile.template

@@ -0,0 +1,32 @@
+#***********************************************************************
+#                   GNU Lesser General Public License
+#
+# This file is part of the GFDL FRE NetCDF tools package (FRE-NCTools).
+#
+# FRE-NCTools is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Lesser General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or (at
+# your option) any later version.
+#
+# FRE-NCTools is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+# FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License
+# for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with FRE-NCTools.  If not, see
+# <http://www.gnu.org/licenses/>.
+#***********************************************************************
+{% extends "container/Dockerfile" %}
+{% block build_stage %}
+{{ super() }}
+{% endblock %}
+{% block final_stage %}
+{{ super() }}
+# Install any needed pip packages
+RUN pip install git+https://github.com/adcroft/numpypi.git && \
+    pip install netCDF4 virtualenv
+# Set compilers for mpich wrappers
+ENV MPICH_FC=gfortran
+ENV MPICH_CC=gcc
+{% endblock %}