Got a working Dockerfile for GNU

Dockerfile.GNU-Linux

@@ -13,40 +13,77 @@
 # dynamically. 
 
 # This build target compiles all dependencies and the swiftest driver itself
-FROM condaforge/mambaforge:23.1.0-4 as build-deps
-ENV SCRIPT_DIR="buildscripts"
+FROM continuumio/miniconda3:23.5.2-0 as build-deps
 SHELL ["/bin/bash", "--login", "-c"]
-ENV SHELL="/bin/bash"
+ENV PATH="/opt/conda/bin:${PATH}"
 WORKDIR /swiftest
 
-# Compile the dependencies
-COPY ./${SCRIPT_DIR}/get_platform.sh ./${SCRIPT_DIR}/
-COPY ./${SCRIPT_DIR}/make_build_environment.sh ./${SCRIPT_DIR}
-COPY ./${SCRIPT_DIR}/build_dependencies.sh ./${SCRIPT_DIR}/
-COPY ./${SCRIPT_DIR}/swiftest-build-env.yml ./${SCRIPT_DIR}/
-COPY ./${SCRIPT_DIR}/fetch_dependencies.sh ./${SCRIPT_DIR}/
-RUN ${SCRIPT_DIR}/fetch_dependencies.sh
-RUN ${SCRIPT_DIR}/make_build_environment.sh && \
-        echo "conda activate swiftest-build-env" >> ~/.bashrc  && \
-        /bin/bash -lic "${SCRIPT_DIR}/build_dependencies.sh GNU-Linux"
+ENV INSTALL_DIR=/usr/local
+ENV NCDIR="${INSTALL_DIR}"
+ENV NFDIR="${INSTALL_DIR}"
+ENV HDF5_ROOT="${INSTALL_DIR}"
+ENV HDF5_LIBDIR="${HDF5_ROOT}/lib"
+ENV HDF5_INCLUDE_DIR="${HDF5_ROOT}/include"
+ENV HDF5_PLUGIN_PATH="${HDF5_LIBDIR}/plugin"
+ENV LD_LIBRARY_PATH="${INSTALL_DIR}/lib"
+ENV LDFLAGS="-L${INSTALL_DIR}/lib"
+ENV CPPFLAGS="-I${INSTALL_DIR}/include"
+
+COPY ./buildscripts/swiftest-build-env.yml ./
+COPY ./buildscripts/fetch_dependencies.sh ./
+RUN ./fetch_dependencies.sh -d ./
+
+# Get the HDF5, NetCDF-C, and NetCDF-Fortran libraries
+RUN conda update --all -y && \
+    conda install conda-libmamba-solver -y && \
+    conda config --set solver libmamba && \
+    conda env create --file swiftest-build-env.yml --name swiftest-build-env && \
+    conda init bash && \
+    echo "conda activate swiftest-build-env" >> ~/.bashrc 
 
-FROM condaforge/mambaforge:23.1.0-4 as build-swiftest
-ENV SCRIPT_DIR="buildscripts"
+RUN cd zlib-* && \
+    ./configure \
+        --prefix=${INSTALL_DIR} \
+        --static && \
+    make && make install && \
+    cd ../hdf5-* && \
+    ./configure \
+        --prefix=${INSTALL_DIR} \
+        --disable-shared \
+        --enable-build-mode=production \
+        --disable-fortran \
+        --disable-java \
+        --disable-cxx \
+        --with-zlib=${INSTALL_DIR} && \
+    make && make install && \
+    cd ../netcdf-c-* && \
+    ./configure \
+        --prefix=${INSTALL_DIR} \
+        --disable-shared \
+        --disable-dap \
+        --disable-libxml2 \
+        --disable-byterange && \
+    make && make install && \
+    cd ../netcdf-fortran-* && \
+    export CFLAGS="-fPIC" && \
+    export FCFLAGS="${CFLAGS}" && \
+    export FFLAGS=${CFLAGS} && \
+    export LIBS=$(${INSTALL_DIR}/bin/nc-config --libs --static) && \
+    ./configure --disable-shared --prefix=${NFDIR} && \
+    make && make install
+
+FROM continuumio/miniconda3:23.5.2-0 as build-swiftest
 SHELL ["/bin/bash", "--login", "-c"]
 ENV SHELL="/bin/bash"
 WORKDIR /swiftest
-ENV BUILD_DIR=/swiftest/build
 
 # Copy build artifacts over to the swiftest package builder stage
-COPY --from=build-deps ${BUILD_DIR}/lib/ /usr/local/lib/
-COPY --from=build-deps ${BUILD_DIR}/include/ /usr/local/include/
-COPY --from=build-deps ${BUILD_DIR}/bin/ /usr/local/bin/
-COPY --from=build-deps ${BUILD_DIR}/share/ /usr/local/share/
+ENV INSTALL_DIR=/usr/local
+COPY --from=build-deps ${INSTALL_DIR}/ ${INSTALL_DIR}/
 COPY --from=build-deps /opt/conda/envs/ /opt/conda/envs/
 COPY --from=build-deps /root/.bashrc /root/
 
 # Compile the Swiftest project
-COPY ./buildscripts/build_swiftest.sh ./buildscripts/
 COPY ./cmake/ ./cmake/
 COPY ./src/ ./src/
 COPY ./swiftest/ ./swiftest/
@@ -56,9 +93,18 @@ COPY ./environment.yml ./
 COPY ./pyproject.toml ./
 COPY ./requirements.txt ./
 COPY ./version.txt ./
+
+# Generate the build environment in conda
 ENV PIP_ROOT_USER_ACTION=ignore
-RUN  /bin/bash -lic "${SCRIPT_DIR}/build_swiftest.sh GNU-Linux /usr/local"
+ENV LDFLAGS="-L${INSTALL_DIR}/lib"
+ENV CFLAGS="-fPIC"
+ENV FFLAGS=${CFLAGS}
+ENV SKBUILD_CONFIGURE_OPTIONS="-DBUILD_SHARED_LIBS=OFF -DMACHINE_CODE_VALUE=\"native\""
+RUN export NFCFG="${INSTALL_DIR}/bin/nf-config" && \
+    export LIBS=$($NFCFG --flibs) && \
+    python3 -m pip install build pip && \
+    python3 -m build --wheel
 
 #Export the generated wheel file to the host machine
 FROM scratch as export-wheel
-COPY --from=build-swiftest /swiftest/dist/ /dist/
+COPY --from=build-swiftest /swiftest/dist/ ./

buildscripts/fetch_dependencies.sh

@@ -12,10 +12,26 @@
 # If not, see: https://www.gnu.org/licenses. 
 SCRIPT_DIR=$(realpath $(dirname $0))
 ROOT_DIR=$(realpath ${SCRIPT_DIR}/..)
-BUILD_DIR="${ROOT_DIR}/build"
-mkdir -p ${BUILD_DIR}
-cd $BUILD_DIR
+# Parse arguments
+USTMT="Usage: ${0} <-d /path/to/download]"
+DOWNLOAD_DIR="${ROOT_DIR}/build"
+while getopts ":d:" ARG; do
+    case "${ARG}" in
+    d)
+        DOWNLOAD_DIR="${OPTARG}"
+        ;;
+    :)      
+        echo "Error: -${OPTARG} requires an argument."
+        echo $USTMT
+        exit 1
+        ;;
+    *)
+        ;;
+    esac
+done
 
+mkdir -p ${DOWNLOAD_DIR}
+cd $DOWNLOAD_DIR
 wget -qO- https://www.zlib.net/zlib-1.2.13.tar.gz | tar xvz
 wget -qO- https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.1/src/hdf5-1.14.1-2.tar.gz | tar xvz 
 wget -qO- https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.9.2.tar.gz | tar xvz 

cmake/Modules/SetFortranFlags.cmake

@@ -144,12 +144,12 @@ IF (NOT BUILD_SHARED_LIBS)
 ENDIF (NOT BUILD_SHARED_LIBS)
 
 IF (USE_SIMD)
-        SET(MACHINE_CODE_VALUE "Host")
 
         IF (COMPILER_OPTIONS STREQUAL "Intel")
+                SET(MACHINE_CODE_VALUE "Host" CACHE STRING "Tells the compiler which processor features it may target, including which instruction sets and optimizations it may generate.")
 
                 IF (MACHINE_CODE_VALUE STREQUAL "generic")
-                        SET(MACHINE_CODE_VALUE "SSE2" FORCE) # SSE2 is the Intel equivalent of generic
+                     SET(MACHINE_CODE_VALUE "SSE2" CACHE STRING "SSE2 is the safest option when compiling for non-host compatibility" FORCE)
                 ENDIF()
 
                 # Enables OpenMP SIMD compilation when OpenMP parallelization is disabled. 
@@ -172,6 +172,7 @@ IF (USE_SIMD)
                                         "/Qvecabi:cmdtarget" # Intel Windows
                                 )
         ELSEIF (COMPILER_OPTIONS STREQUAL "GNU")
+                SET(MACHINE_CODE_VALUE "native" CACHE STRING "Tells the compiler which processor features it may target, including which instruction sets and optimizations it may generate.")
 
                 # Enables OpenMP SIMD compilation when OpenMP parallelization is disabled. 
                 IF (NOT USE_OPENMP)
@@ -180,8 +181,8 @@ IF (USE_SIMD)
                         )     
                 ENDIF (NOT USE_OPENMP)
 
-                IF (MACHINE_CODE_VALUE STREQUAL "host")
-                        SET(MACHINE_CODE_VALUE "native" CACHE STRING "Tells the compiler which processor features it may target, including which instruction sets and optimizations it may generate.")
+                IF (MACHINE_CODE_VALUE STREQUAL "Host")
+                        SET(MACHINE_CODE_VALUE "native" CACHE STRING "native is the GNU equivalent of Host" FORCE)
                 ENDIF ()
 
                 IF (APPLE)
@@ -192,6 +193,9 @@ IF (USE_SIMD)
                         SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}"
                                         Fortran "-march=${MACHINE_CODE_VALUE}" 
                         )
+                        SET_COMPILE_FLAG(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS}"
+                                        Fortran "-mtune=${MACHINE_CODE_VALUE}" 
+                        )
                 ENDIF ()
 
         ENDIF ()

setup.py

@@ -14,7 +14,6 @@
 
 cmake_args = [
             '-DCMAKE_BUILD_TYPE=RELEASE',
-            '-DMACHINE_CODE_VALUE="generic"',
             '-DUSE_COARRAY:BOOL=OFF',
             '-DUSE_OPENMP:BOOL=ON',
             ]

src/CMakeLists.txt

@@ -34,7 +34,6 @@ ENDIF ()
 # RELEASE, PROFILING, and TESTING.  
 INCLUDE(SetFortranFlags) 
 
-
 # Add the source files
 SET(STRICT_MATH_FILES
             ${SRC}/collision/collision_generate.f90