remove separate build stage and use hybrid apt-get + spack

docker/ubuntu

@@ -1,25 +1,20 @@
 # Build stage with Spack pre-installed and ready to be used
-FROM spack/ubuntu-jammy:develop AS builder
+FROM spack/ubuntu-jammy:develop
+
+# Get Ubuntu packages
+RUN apt-get update \
+&& apt-get upgrade \
+&& apt-get install -y python3-dev python-is-python3 \
+    build-essential cmake vim emacs wget \
+&& apt-get clean \
+&& rm -rf /var/lib/apt/lists/*
 
 # What we want to install and how we want to install it
 # is specified in a manifest file (spack.yaml)
 RUN mkdir -p /opt/spack-environment && \
 set -o noclobber \
 &&  (echo spack: \
 &&   echo '  specs:' \
-&&   echo '  - cmake' \
-&&   echo '  - vim' \
-&&   echo '  - emacs' \
-&&   echo '  - wget' \
-&&   echo '  - py-pip' \
-&&   echo '  - py-numpy@1.25' \
-&&   echo '  - py-pyaml' \
-&&   echo '  - py-polars' \
-&&   echo '  - py-pandas~performance' \
-&&   echo '  - py-matplotlib' \
-&&   echo '  - mesa~llvm' \
-&&   echo '  - vtk~mpi~opengl2+python' \
-&&   echo '  - py-h5py' \
 &&   echo '  - exaca@master' \
 &&   echo '  - additivefoam@main' \
 &&   echo '  concretizer:' \
@@ -28,22 +23,22 @@ set -o noclobber \
 &&   echo '    install_tree: /opt/software' \
 &&   echo '  view: /opt/views/view') > /opt/spack-environment/spack.yaml
 
-# Install the software
-RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast
-
-# Strip all the binaries
-RUN find -L /opt/views/view/* -type f -exec readlink -f '{}' \; | \
+# Build the spack environment
+RUN cd /opt/spack-environment \
+&& spack env activate . \
+&& spack external find \
+&& spack install --fail-fast \
+&& find -L /opt/views/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
+    awk -F: '{print $1}' | xargs strip \
+&& spack gc -y
 
 # Modifications to the environment that are necessary to run
 RUN cd /opt/spack-environment && \
     spack env activate --sh -d . > activate.sh
 
-
-# This section should eventually be moved into spack installs
 # Install 3DThesis
 ENV THESIS_DIR=/opt/3DThesis
 RUN . /opt/spack-environment/activate.sh && \
@@ -53,47 +48,15 @@ RUN . /opt/spack-environment/activate.sh && \
     wget --quiet ${THESIS_URL} --output-document=${THESIS_ARCHIVE} && \
     mkdir -p 3dthesis && \
     tar -xf ${THESIS_ARCHIVE} -C 3dthesis --strip-components=1 && \
+    rm -f ${THESIS_ARCHIVE} && \
     cd 3dthesis && \
     cmake -B build \
       -D CMAKE_INSTALL_PREFIX=${THESIS_DIR} \
       -D CMAKE_BUILD_TYPE=Debug && \
     cmake --build build && \
     cmake --install build
-RUN echo 'PATH="/opt/3DThesis/bin:$PATH"' >> activate.sh
+RUN echo 'export PATH="/opt/3DThesis/bin:$PATH"' >> activate.sh
 
-# Get Mist
-ENV MIST_DIR=/opt/mist
-RUN . /opt/spack-environment/activate.sh && \
-    MIST_VERSION=main.tar.gz && \
-    MIST_ARCHIVE=mist-${MIST_VERSION} && \
-    MIST_URL=https://github.com/ORNL-MDF/Mist/archive/refs/heads/${MIST_VERSION} && \
-    wget --quiet ${MIST_URL} --output-document=${MIST_ARCHIVE} && \
-    mkdir -p ${MIST_DIR} && \
-    tar -xf ${MIST_ARCHIVE} -C ${MIST_DIR} --strip-components=1 && \
-    python3 -m pip --upgrade && \
-    python3 -m pip install ${MIST_DIR} --root-user-action=ignore
-# Get bnpy
-ENV BNPY_DIR=/opt/bnpy
-RUN . /opt/spack-environment/activate.sh && \
-    BNPY_VERSION=master.tar.gz && \
-    BNPY_ARCHIVE=bnpy-${BNPY_VERSION} && \
-    BNPY_URL=https://github.com/gknapp1/bnpy/archive/refs/heads/${BNPY_VERSION} && \
-    wget --quiet ${BNPY_URL} --output-document=${BNPY_ARCHIVE} && \
-    mkdir -p ${BNPY_DIR} && \
-    tar -xf ${BNPY_ARCHIVE} -C ${BNPY_DIR} --strip-components=1 && \
-    python3 -m pip --upgrade && \
-    python3 -m pip install ${BNPY_DIR} --root-user-action=ignore
-# Get pyebsd
-ENV PYEBSD_DIR=/opt/pyebsd
-RUN . /opt/spack-environment/activate.sh && \
-    PYEBSD_VERSION=master.tar.gz && \
-    PYEBSD_ARCHIVE=pyebsd-${PYEBSD_VERSION} && \
-    PYEBSD_URL=https://github.com/arthursn/pyebsd/archive/refs/heads/${PYEBSD_VERSION} && \
-    wget --quiet ${PYEBSD_URL} --output-document=${PYEBSD_ARCHIVE} && \
-    mkdir -p ${PYEBSD_DIR} && \
-    tar -xf ${PYEBSD_ARCHIVE} -C ${PYEBSD_DIR} --strip-components=1 && \
-    python3 -m pip --upgrade && \
-    python3 -m pip install ${PYEBSD_DIR} --root-user-action=ignore
 # Get Myna
 ENV MYNA_DIR=/opt/myna
 RUN . /opt/spack-environment/activate.sh && \
@@ -103,27 +66,12 @@ RUN . /opt/spack-environment/activate.sh && \
     wget --quiet ${MYNA_URL} --output-document=${MYNA_ARCHIVE} && \
     mkdir -p ${MYNA_DIR} && \
     tar -xf ${MYNA_ARCHIVE} -C ${MYNA_DIR} --strip-components=1 && \
+    rm -f ${MYNA_ARCHIVE} && \
     python3 -m pip --upgrade && \
-    python3 -m pip install ${MYNA_DIR} --root-user-action=ignore
-
-# Clean up packages
-RUN spack gc -y
-
-
-# Bare OS image to run the installed executables
-FROM ubuntu:22.04
-
-COPY --from=builder /opt/spack-environment /opt/spack-environment
-COPY --from=builder /opt/software /opt/software
-COPY --from=builder /opt/3DThesis /opt/3DThesis
-COPY --from=builder /opt/mist /opt/mist
-COPY --from=builder /opt/bnpy /opt/bnpy
-COPY --from=builder /opt/pyebsd /opt/pyebsd
-COPY --from=builder /opt/myna /opt/myna
-
-# paths.view is a symlink, so copy the parent to avoid dereferencing and duplicating it
-COPY --from=builder /opt/views /opt/views
+    python3 -m pip install ${MYNA_DIR} --root-user-action=ignore && \
+    python3 -m pip cache purge
 
+# Set entry point
 RUN { \
       echo '#!/bin/sh' \
       && echo '.' /opt/spack-environment/activate.sh \
@@ -132,7 +80,5 @@ RUN { \
 && chmod a+x /entrypoint.sh \
 && ln -s /opt/views/view /opt/view
 
-
 ENTRYPOINT [ "/entrypoint.sh" ]
-CMD [ "/bin/bash" ]
-
+CMD [ "/bin/bash" ]

spack.yaml

@@ -1,21 +1,5 @@
 spack:
   specs:
-  - cmake
-  - vim
-  - emacs
-  - wget
-  # (can eventually be removed with myna install)
-  - py-pip
-  - py-numpy@1.25
-  - py-pyaml
-  - py-polars
-  # Enabling "performance" substantially increases build times
-  - py-pandas~performance
-  - py-matplotlib
-  # Only to simplify the stack (vtk dep)
-  - mesa~llvm
-  - vtk~mpi~opengl2+python
-  - py-h5py
   # Myna apps (can eventually be replaced with "myna +exaca +additivefoam")
   - exaca@master
   - additivefoam@main