Simplified single-stage Dockerfile

Dockerfile

@@ -1,28 +1,27 @@
-FROM ubuntu:22.04 as build
+FROM eclipse-temurin:17-jdk-jammy
 
 RUN apt-get -y update && apt-get install -y apt-utils && \
     apt-get install -y -qq -o=Dpkg::Use-Pty=0 build-essential gfortran zlib1g-dev \
-    libhdf5-dev libcurl4-openssl-dev libboost-dev cmake wget python3
+    libhdf5-dev libcurl4-openssl-dev libboost-dev cmake wget python3 && \
+    apt-get install -q -y --no-install-recommends curl dnsutils
 
-##
-## build PETSc with mpich for static linking
-##
-#RUN mkdir /usr/local/petsc && \
-#    cd /usr/local/petsc && \
-#    wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.7.7.tar.gz && \
-#    tar xzf petsc-3.7.7.tar.gz && \
-#    cd petsc-3.7.7 && \
-#    ./configure --with-shared-libraries=0 --download-fblaslapack=1 --with-debugging=1 --download-mpich && \
-#    make PETSC_DIR=/usr/local/petsc/petsc-3.7.7 PETSC_ARCH=arch-linux2-c-debug all
+# Create a custom Java runtime
+RUN $JAVA_HOME/bin/jlink \
+         --add-modules ALL-MODULE-PATH \
+         --strip-debug \
+         --no-man-pages \
+         --no-header-files \
+         --compress=2 \
+         --output /javaruntime
+
+ENV JAVA_HOME=/javaruntime
+ENV PATH="${JAVA_HOME}/bin:${PATH}"
 
-#ENV PETSC_DIR=/usr/local/petsc/petsc-3.7.7 \
-#    PETSC_ARCH=arch-linux2-c-debug
+ENV DEBIAN_FRONTEND=noninteractive
+ENV LANG=en_US.UTF-8
 
 COPY . /vcellroot
 
-#
-# build most solvers, and FiniteVolume without PETSc (FiniteVolume_x64)
-#
 RUN mkdir -p /vcellroot/build/bin
 WORKDIR /vcellroot/build
 
@@ -41,62 +40,8 @@ RUN /usr/bin/cmake \
     -DOPTION_TARGET_HY3S_SOLVERS=OFF \
     .. && \
     make && \
-    ctest -VV
-
-##
-## build FiniteVolume with PETSc (FiniteVolume_PETSc_x64)
-##
-#RUN mkdir -p /vcellroot/build_PETSc/bin
-#WORKDIR /vcellroot/build_PETSc
-#
-#RUN /usr/bin/cmake \
-#    -DOPTION_TARGET_MESSAGING=ON \
-#    -DOPTION_TARGET_PARALLEL=OFF \
-#    -DOPTION_TARGET_PETSC=ON \
-#    -DOPTION_TARGET_CHOMBO2D_SOLVER=OFF \
-#    -DOPTION_TARGET_CHOMBO3D_SOLVER=OFF \
-#    -DOPTION_TARGET_SMOLDYN_SOLVER=OFF \
-#    -DOPTION_TARGET_FV_SOLVER=ON \
-#    -DOPTION_TARGET_STOCHASTIC_SOLVER=OFF \
-#    -DOPTION_TARGET_NFSIM_SOLVER=OFF \
-#    -DOPTION_TARGET_MOVINGBOUNDARY_SOLVER=OFF \
-#    -DOPTION_TARGET_SUNDIALS_SOLVER=OFF \
-#    -DOPTION_TARGET_HY3S_SOLVERS=OFF \
-#    .. && \
-#    make && \
-#    ctest
-
-
-FROM eclipse-temurin:17 as jre-build
-
-# Create a custom Java runtime
-RUN $JAVA_HOME/bin/jlink \
-         --add-modules ALL-MODULE-PATH \
-         --strip-debug \
-         --no-man-pages \
-         --no-header-files \
-         --compress=2 \
-         --output /javaruntime
+    ctest -VV && \
+    mv /vcellroot/build/bin /vcellbin
 
-# Define base image and copy in jlink created minimal Java 17 environment
-FROM python:3.9.7-slim
-ENV JAVA_HOME=/opt/java/openjdk
-ENV PATH "${JAVA_HOME}/bin:${PATH}"
-COPY --from=jre-build /javaruntime $JAVA_HOME
-
-# now we have Java 17 and Python 3.9
-ENV DEBIAN_FRONTEND noninteractive
-ENV LANG=en_US.UTF-8
-
-RUN apt-get update && \
-    apt-get install -y apt-utils && \
-    apt-get install -q -y --no-install-recommends curl dnsutils
-
-RUN apt-get install -qq -y -o=Dpkg::Use-Pty=0 gcc gfortran zlib1g \
-    libhdf5-103 libhdf5-cpp-103 libcurl4-openssl-dev zip
-
-COPY --from=build /vcellroot/build/bin /vcellbin
-#COPY --from=build /vcellroot/build_PETSc/bin/FiniteVolume_PETSc_x64 /vcellbin/
 WORKDIR /vcellbin
 ENV PATH=/vcellbin:$PATH
-