Enable using split schism domains

.gitignore

@@ -79,3 +79,6 @@ dist/
 
 venv
 .venv
+.idea
+
+/git_info.json

.gitlab-ci.yml

@@ -0,0 +1,117 @@
+# GitLab CI/CD configuration file for ngen-forcing repository
+include:
+  - template: Jobs/Container-Scanning.gitlab-ci.yml
+
+stages:
+  - build
+  - unit_test
+  - sonarqube
+  - test
+  - deploy
+
+image: registry.sh.nextgenwaterprediction.com/infrastructure/docker/docker:latest
+
+variables:
+    DOCKER_IMAGE_NAME_BMI_FORCING: $CI_REGISTRY_IMAGE/ngen-bmi-forcing
+    DOCKER_IMAGE_NAME_LUMPED_FORCING: $CI_REGISTRY_IMAGE/ngen-lumped-forcing
+    DOCKER_IMAGE_NAME_COASTAL: $CI_REGISTRY_IMAGE/ngen-coastal
+    DOCKER_IMAGE_TAG: $CI_COMMIT_REF_NAME
+
+build:
+  stage: build
+  script:
+    - echo "Logging in to Gitlab Container Registry..."
+    - echo $CI_JOB_TOKEN | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
+    - echo "Building ${CI_PROJECT_NAME} docker images.. "
+    - docker build --file=Dockerfile.bmi-forcings --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --tag "$DOCKER_IMAGE_NAME_BMI_FORCING:$DOCKER_IMAGE_TAG" .
+    - docker push $DOCKER_IMAGE_NAME_BMI_FORCING:$DOCKER_IMAGE_TAG
+    - docker build --file=Dockerfile.lumped-forcings --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --tag "$DOCKER_IMAGE_NAME_LUMPED_FORCING:$DOCKER_IMAGE_TAG" .
+    - docker push $DOCKER_IMAGE_NAME_LUMPED_FORCING:$DOCKER_IMAGE_TAG
+    - docker build --secret id=GITLAB_TOKEN,env=GITLAB_TOKEN --file=Dockerfile.ngencoastal --build-arg CI_COMMIT_REF_NAME=${CI_COMMIT_REF_NAME} --tag "$DOCKER_IMAGE_NAME_COASTAL:$DOCKER_IMAGE_TAG" .
+    - docker push $DOCKER_IMAGE_NAME_COASTAL:$DOCKER_IMAGE_TAG
+    - docker logout
+
+unit-test-bmi:
+  stage: unit_test
+  image: $DOCKER_IMAGE_NAME_BMI_FORCING:$DOCKER_IMAGE_TAG
+  script:
+    # TODO add unit tests when available
+    - echo "Running BMI Forcing Unit Tests..."
+
+unit-test-lumped:
+  stage: unit_test
+  image: $DOCKER_IMAGE_NAME_LUMPED_FORCING:$DOCKER_IMAGE_TAG
+  script:
+    # TODO add unit tests when available
+    - echo "Running Lumped Forcing Unit Tests..."
+
+unit-test-coastal:
+  stage: unit_test
+  image: $DOCKER_IMAGE_NAME_COASTAL:$DOCKER_IMAGE_TAG
+  script:
+    # TODO add unit tests when available
+    - echo "Running Coastal Unit Tests..."
+
+sonarqube:
+  stage: sonarqube
+  image:
+    name: registry.sh.nextgenwaterprediction.com/infrastructure/sonar-scanner-cli/sonar-scanner-cli:5.0.1
+    entrypoint: [""]
+  variables:
+    # Defines the location of the analysis task cache
+    SONAR_USER_HOME: "${CI_PROJECT_DIR}/.sonar"
+    # Shallow cloning needs to be disabled.
+    # See https://docs.sonarqube.org/latest/analysis/gitlab-cicd/.
+    GIT_DEPTH: 0
+  cache:
+    key: "${CI_JOB_NAME}"
+    paths:
+      - .sonar/cache
+  script:
+    - sonar-scanner -X -Dsonar.verbose=true
+  allow_failure: true # FIXME
+
+container_scanning:
+  stage: test
+  needs:
+    - build
+  variables:
+    SECURE_LOG_LEVEL: info
+    CS_SEVERITY_THRESHOLD: UNKNOWN
+    CS_IMAGE: $DOCKER_IMAGE_NAME_BMI_FORCING:$DOCKER_IMAGE_TAG
+
+container_scanning_2:
+  extends: container_scanning
+  stage: test
+  needs:
+    - build
+  variables:
+    SECURE_LOG_LEVEL: info
+    CS_SEVERITY_THRESHOLD: UNKNOWN
+    CS_IMAGE: $DOCKER_IMAGE_NAME_LUMPED_FORCING:$DOCKER_IMAGE_TAG
+
+container_scanning_3:
+  extends: container_scanning
+  stage: test
+  needs:
+    - build
+  variables:
+    SECURE_LOG_LEVEL: info
+    CS_SEVERITY_THRESHOLD: UNKNOWN
+    CS_IMAGE: $DOCKER_IMAGE_NAME_COASTAL:$DOCKER_IMAGE_TAG
+
+deploy:
+  stage: deploy
+  script:
+    - echo "Logging in to Gitlab Container Registry to push the image..."
+    - echo $CI_JOB_TOKEN | docker login -u $CI_REGISTRY_USER --password-stdin $CI_REGISTRY
+    - echo "Pushing to the docker registry"
+    - docker tag $DOCKER_IMAGE_NAME_BMI_FORCING:$DOCKER_IMAGE_TAG $DOCKER_IMAGE_NAME_BMI_FORCING:latest
+    - docker push $DOCKER_IMAGE_NAME_BMI_FORCING:latest
+    - docker tag $DOCKER_IMAGE_NAME_LUMPED_FORCING:$DOCKER_IMAGE_TAG $DOCKER_IMAGE_NAME_LUMPED_FORCING:latest
+    - docker push $DOCKER_IMAGE_NAME_LUMPED_FORCING:latest
+    - docker tag $DOCKER_IMAGE_NAME_COASTAL:$DOCKER_IMAGE_TAG $DOCKER_IMAGE_NAME_COASTAL:latest
+    - docker push $DOCKER_IMAGE_NAME_COASTAL:latest
+    - docker logout
+  rules:
+    - if: '$CI_COMMIT_BRANCH == "development"'

DOCKER.md

@@ -0,0 +1,63 @@
+# How to use ngen-forcing Docker containers
+
+The Dockerfiles within this project will allow you to run the scripts from the ngen-forcing repository. There are 2 Docker container images that can be built:
+1. NextGen_Forcings_Engine_BMI
+1. NextGen_Lumped_Forcings_Driver
+
+## Requirements
+
+To build and run these containers, you will need the following software installed and running on your system:
+- Docker Engine
+
+## Building NextGen_Forcings_Engine_BMI
+
+To build the NextGen_Forcings_Engine_BMI container, execute the following command:
+```
+docker build --file=Dockerfile.bmi-forcings --tag=ngen-bmi-forcing .
+```
+
+## Building NextGen_Lumped_Forcings_Driver
+
+To build the NextGen_Lumped_Forcings_Driver container, execute the following command:
+```
+docker build --file=Dockerfile.lumped-forcings --tag=ngen-lumped-forcing .
+```
+
+## Running NextGen_Forcings_Engine_BMI
+
+To run the NextGen_Forcings_Engine_BMI container, execute the following command:
+```
+docker run -it ngen-bmi-forcing
+```
+This will drop you to a bash prompt inside the container.
+
+You will next need to activate the required conda environment:
+```
+conda activate /ngen-app/conda
+```
+All the ngen-forcing scripts are located at `/ngen-app/ngen-forcing/`.
+
+
+## Running NextGen_Lumped_Forcings_Driver
+
+To run the NextGen_Lumped_Forcings_Driver container, execute the following command:
+```
+docker run -it ngen-lumped-forcing
+```
+This will drop you to a bash prompt inside the container.
+
+You will next need to activate the required conda environment:
+```
+conda activate /ngen-app/conda
+```
+All the ngen-forcing scripts are located at `/ngen-app/ngen-forcing/`.
+
+## Troubleshooting
+
+Troubleshooting information and procedures will be added as we further improve these containers.
+
+## Future Improvements 
+
+- Make sure conda environments are activating automatically and don't have to be activated as a separate step
+- Add entrypoint scripts that make it easier to execute these scripts
+- Replace specialized fork of ExactExtract python package with official release

Dockerfile.bmi-forcings

@@ -0,0 +1,185 @@
+## TODO: replace with base image created under NGWPC-3223 ##
+## see: https://jira.nextgenwaterprediction.com/browse/NGWPC-3223
+FROM rockylinux:8
+
+# ensure local python is preferred over distribution python
+ENV PATH="/usr/local/bin:$PATH"
+
+# cannot remove LANG even though https://bugs.python.org/issue19846 is fixed
+# last attempted removal of LANG broke many users:
+# https://github.com/docker-library/python/pull/570
+ENV LANG="C.UTF-8"
+
+## FIXME: Replace installation and build of FOSS dependencies wiith a base image. ##
+
+# runtime dependencies
+RUN set -eux; \
+    dnf install -y dnf-plugins-core; \
+    dnf install -y epel-release; \
+    dnf config-manager --set-enabled powertools; \
+    dnf install -y \
+        proj proj-devel \
+        sqlite sqlite-devel \
+        autoconf \
+        automake \
+        bzip2 bzip2-devel \
+        cmake \
+        curl curl-devel \
+        file \
+        findutils \
+        git \
+        jq \
+## FIXME: replace GNU compilers with Intel compiler ##
+        gcc-toolset-10 \
+        gcc-toolset-10-libasan-devel \
+        gcc-toolset-10-gcc-gfortran \
+        jasper-libs jasper-devel \
+        libaec libaec-devel \
+        libasan6 \
+        libffi libffi-devel \
+        libpng libpng-devel \
+        m4 \
+## FIXME: replace openmpi with Intel MPI libraries ##
+        openmpi openmpi-devel \
+        openssl openssl-devel \
+        python3.11 \
+        python3.11-devel \
+        python3.11-pip \
+        python3.11-pyyaml \
+        rsync \
+        uuid uuid-devel \
+        which \
+        zlib zlib-devel \
+        hdf5-devel \
+        netcdf-devel \
+        netcdf-fortran-devel \
+    ; \
+    dnf clean all
+
+## FIXME: replace GNU compilers with Intel compiler ##
+SHELL [ "/usr/bin/scl", "enable", "gcc-toolset-10"]
+## FIXME: replace openmpi with Intel MPI libraries ##
+ENV PATH="${PATH}:/usr/lib64/openmpi/bin/"
+
+RUN set -eux; \
+    curl --location --output wgrib2.tgz "https://ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/wgrib2.tgz" ; \
+    mkdir --parents /usr/src/wgrib2 ; \
+    tar --extract --directory /usr/src/wgrib2 --strip-components=1 --file wgrib2.tgz ; \
+    rm wgrib2.tgz ; \
+    cd /usr/src/wgrib2 ; \
+    export CC=gcc ; \
+    export FC=gfortran ; \
+    make \
+        USE_IPOLATES=3 \
+        USE_PNG=1 \
+        USE_AEC=0 \
+        USE_JASPER=1 \
+        USE_OPENJPEG=0 \
+        USE_G2CLIB=0 \
+        PREFIX=/usr/local ; \
+    make lib ; \
+    cp /usr/src/wgrib2/wgrib2/wgrib2 /usr/local/bin/ ; \
+    chmod +x /usr/local/bin/wgrib2 ; \
+    rm --recursive --force /usr/src/wgrib2
+
+# Build and install ESMF 8.8.0
+RUN set -eux; \
+    curl --location --output esmf-8.8.0.tar.gz "https://github.com/esmf-org/esmf/archive/refs/tags/v8.8.0.tar.gz"; \
+    tar --extract --gzip --file esmf-8.8.0.tar.gz; \
+    rm esmf-8.8.0.tar.gz; \
+    cd esmf-8.8.0; \
+    export ESMF_DIR=/esmf-8.8.0; \
+    export ESMF_INSTALL_PREFIX=/usr/local/esmf; \
+    export ESMF_COMPILER=gfortran; \
+    export ESMF_COMM=openmpi; \
+    export ESMF_NETCDF="nc-config"; \
+    export ESMF_F90COMPILEPATHS="-I/usr/lib64/gfortran/modules"; \
+    export ESMF_BOPT=O; \
+    make all; \
+    make install; \
+    cd ..; \
+    rm -rf esmf-8.8.0
+
+# Build GDAL from source
+RUN --mount=type=cache,target=/root/.cache/gdal,id=gdal-build \
+    set -eux && \
+    curl --location --output gdal.tar.gz https://github.com/OSGeo/gdal/releases/download/v3.7.3/gdal-3.7.3.tar.gz && \
+    mkdir --parents /usr/src/gdal && \
+    tar --extract --directory /usr/src/gdal --strip-components=1 --file gdal.tar.gz && \
+    cd /usr/src/gdal && \
+    cmake -B build -S . -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local && \
+    cmake --build build --parallel "$(nproc)" && \
+    cmake --build build --target install && \
+    ldconfig && \
+    rm --recursive --force /usr/src/gdal gdal.tar.gz
+
+# -------------------------------
+# Create a self-contained venv for ngen-forcing
+# -------------------------------
+ENV VIRTUAL_ENV="/ngen-app/ngen-python"
+RUN python3.11 -m venv ${VIRTUAL_ENV}
+ENV PATH="${VIRTUAL_ENV}/bin:${PATH}" \
+    PYTHONPATH="${VIRTUAL_ENV}/lib/python3.11/site-packages"
+
+# Install ESMPy
+ENV ESMFMKFILE=/usr/local/esmf/lib/libO/Linux.gfortran.64.openmpi.default/esmf.mk
+RUN set -eux; \
+    pip3.11 install setuptools-git-versioning; \
+    git clone --depth 1 --branch v8.8.0 https://github.com/esmf-org/esmf.git; \
+    cd esmf/src/addon/esmpy; \
+    python3.11 -m pip install .; \
+    cd /; \
+    rm -rf esmf
+
+
+ENV PATH="/usr/local/bin:${PATH}"
+
+ENV WGRIB2=/usr/local/bin/wgrib2
+
+# Fix OpenMPI transport for containers
+ENV OMPI_MCA_btl_vader_single_copy_mechanism=none
+ENV OMPI_MCA_btl=^openib,ofi
+ENV OMPI_MCA_pml=ob1
+ENV OMPI_MCA_btl_base_warn_component_unused=0
+
+################################################
+
+# Reset SHELL so we're not locked into the gcc-10 build environment
+SHELL ["/bin/bash", "-c"]
+
+COPY . /ngen-app/ngen-forcing/
+
+# Install ngen-forcing as a Python package
+WORKDIR /ngen-app/ngen-forcing
+RUN set -eux; \
+    pip install --upgrade pip setuptools wheel; \
+    pip install --no-cache-dir mpi4py . ./nextgen_forcings_ewts
+
+ARG CI_COMMIT_REF_NAME
+
+RUN set -eux; \
+    # Get the remote URL from Git configuration
+    repo_url=$(git config --get remote.origin.url); \
+    # Extract the repo name (everything after the last slash) and remove any trailing .git
+    key=${repo_url##*/}; \
+    key=${key%.git}; \
+    # ngen-forcing is different from the other repos.  We don't use the repo name directly
+    GIT_INFO_PATH="/ngen-app/ngen-bmi-forcing_git_info.json"; \
+    # Determine branch name: use CI_COMMIT_REF_NAME if set; otherwise, use git's current branch
+    branch=$( [ -n "${CI_COMMIT_REF_NAME:-}" ] && echo "${CI_COMMIT_REF_NAME}" || git rev-parse --abbrev-ref HEAD ); \
+    jq -n \
+      --arg commit_hash "$(git rev-parse HEAD)" \
+      --arg branch "$branch" \
+      --arg tags "$(git tag --points-at HEAD | tr '\n' ' ')" \
+      --arg author "$(git log -1 --pretty=format:'%an')" \
+      --arg commit_date "$(date -u -d @$(git log -1 --pretty=format:'%ct') +'%Y-%m-%d %H:%M:%S UTC')" \
+      --arg message "$(git log -1 --pretty=format:'%s' | tr '\n' ';')" \
+      --arg build_date "$(date -u +'%Y-%m-%d %H:%M:%S UTC')" \
+      "{\"ngen-bmi-forcing\": {commit_hash: \$commit_hash, branch: \$branch, tags: \$tags, author: \$author, commit_date: \$commit_date, message: \$message, build_date: \$build_date}}" \
+      > $GIT_INFO_PATH
+
+WORKDIR /
+
+ENV LD_LIBRARY_PATH="/usr/lib64/openmpi/lib/"
+
+ENTRYPOINT [ "/bin/bash" ]