#76 Add Dockerfile.system

Author: kwabenantim

.github/workflows/docker-portability-system.yml

@@ -19,15 +19,7 @@ jobs:
         include:
           - tags: |
               chaste/runner:${{ github.event.inputs.ubuntu_release }}.portability-system
-            build-args: |
-              BASE=${{ github.event.inputs.ubuntu_release }}
-              XSD=system
-              XERCESC=system
-              SUNDIALS=system
-              BOOST=system
-              VTK=system
-              PETSC=system
-              HDF5=system
+            build-args: BASE=${{ github.event.inputs.ubuntu_release }}
 
     steps:
       - name: Checkout
@@ -49,6 +41,7 @@ jobs:
         uses: docker/build-push-action@v5
         with:
           context: .
+          file: ./Dockerfile.system
           pull: true
           load: true
           tags: ${{ matrix.tags }}

Dockerfile

@@ -1,3 +1,12 @@
+# Build the image:
+# docker build -t chaste/runner:portability-test .
+
+# Run the container in interactive mode:
+# docker run --init -it -e RUNNER_OFF=1 chaste/runner:portability-test /bin/bash
+
+# Run the container:
+# docker run --init -it chaste/runner:portability-test
+
 ARG BASE=jammy
 
 FROM ubuntu:${BASE}
@@ -14,13 +23,15 @@ SHELL ["/bin/bash", "-e", "-o", "pipefail", "-c"]
 
 USER root
 
+# Setup base dependencies and install actions runner
+
 ENV DEFAULT_USER="runner" \
     DEFAULT_HOME="/home/runner" \
     RUNNER_DIR="/home/runner/actions-runner" \
     RUNNER_WORK_DIR="/home/runner/_work" \
     MODULES_DIR="/home/runner/modules"
 
-COPY scripts/ /usr/local/bin/
+COPY scripts/custom/ /usr/local/bin/
 
 RUN useradd -r -m -d ${DEFAULT_HOME} -s /bin/bash ${DEFAULT_USER} && \
     os_id="$(. /etc/os-release && echo ${VERSION_ID} | sed 's/\.//')" && \
@@ -36,6 +47,8 @@ RUN useradd -r -m -d ${DEFAULT_HOME} -s /bin/bash ${DEFAULT_USER} && \
 USER ${DEFAULT_USER}:${DEFAULT_USER}
 WORKDIR ${DEFAULT_HOME}
 
+# Build Chaste dependencies from source
+
 RUN source /etc/profile.d/modules.sh && \
     mkdir -p ${MODULES_DIR}/modulefiles && \
     module use ${MODULES_DIR}/modulefiles && \

Dockerfile.system

@@ -0,0 +1,56 @@
+# Build the image:
+# docker build -t chaste/runner:portability-system .
+
+# Run the container in interactive mode:
+# docker run --init -it -e RUNNER_OFF=1 chaste/runner:portability-system /bin/bash
+
+# Run the container:
+# docker run --init -it chaste/runner:portability-system
+
+ARG BASE=jammy
+
+FROM ubuntu:${BASE}
+
+SHELL ["/bin/bash", "-e", "-o", "pipefail", "-c"]
+
+USER root
+
+# Setup Chaste dependencies and install actions runner
+
+ENV DEFAULT_USER="runner" \
+    DEFAULT_HOME="/home/runner" \
+    RUNNER_DIR="/home/runner/actions-runner" \
+    RUNNER_WORK_DIR="/home/runner/_work" \
+    MODULES_DIR="/home/runner/modules"
+
+COPY scripts/system/ /usr/local/bin/
+
+RUN useradd -r -m -d ${DEFAULT_HOME} -s /bin/bash ${DEFAULT_USER} && \
+    os_id="$(. /etc/os-release && echo ${VERSION_ID} | sed 's/\.//')" && \
+    setup_ubuntu${os_id}.sh && \
+    runner_install.sh --install_dir="/tmp/tmp-runner" && \
+    /tmp/tmp-runner/bin/installdependencies.sh && \
+    apt-get -y clean && \
+    rm -rf /var/cache/apt && \
+    rm -rf /var/lib/apt/lists/* && \
+    rm -rf /var/tmp/* && \
+    rm -rf /tmp/*
+
+USER ${DEFAULT_USER}:${DEFAULT_USER}
+WORKDIR ${DEFAULT_HOME}
+
+# Add modulefile stubs for system dependency versions
+
+RUN source /etc/profile.d/modules.sh && \
+    mkdir -p ${MODULES_DIR}/modulefiles && \
+    module use ${MODULES_DIR}/modulefiles && \
+    echo "module use ${MODULES_DIR}/modulefiles" >> ${DEFAULT_HOME}/.bashrc && \
+    install_modulefiles.sh --modules-dir=${MODULES_DIR} && \
+    module test boost && \
+    module test xsd && \
+    module test xercesc && \
+    module test petsc_hdf5 && \
+    module test sundials && \
+    module test vtk
+
+ENTRYPOINT ["docker-entrypoint.sh"]