Merge pull request #317 from EDmodel/dockerization

Add ability to create ED docker image

.github/workflows/docker.yml

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+name: Docker
+
+# This will run when:
+# - when new code is pushed to master to push the tags latest.
+# - when a pull request is created and updated  to make sure the
+#   Dockerfile is still valid.
+
+# To be able to push to dockerhub, this expects the following
+# secrets to be set in the project:
+# - DOCKERHUB_USERNAME : username that can push to the org
+# - DOCKERHUB_PASSWORD : password asscoaited with the username
+
+# To be able to push to github, this expects the following
+# secrets to be set in the project:
+# - GHCR_USERNAME : username that can push to the org
+# - GHCR_PASSWORD : password asscoaited with the username
+
+on:
+  push:
+    branches:
+      - master
+
+  pull_request:
+
+# Certain actions will only run when this is the master repo.
+env:
+  MASTER_REPO: EDModel/ED2
+  DOCKERHUB_ORG: pecan
+
+jobs:
+  docker:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v2
+
+      # calculate some variables that are used later
+      - name: github branch
+        run: |
+          BRANCH=${GITHUB_REF##*/}
+          if [ "$BRANCH" == "master" ]; then
+            TAGS="latest"
+          else
+            TAGS="$BRANCH"
+          fi
+          echo "TAGS=${TAGS}" >> $GITHUB_ENV
+          echo "GITHUB_BRANCH=${BRANCH}" >> $GITHUB_ENV
+
+      # build the docker image, this will always run to make sure
+      # the Dockerfile still works.
+      - name: Build image
+        uses: elgohr/[email protected]
+        env:
+          BRANCH: ${{ env.GITHUB_BRANCH }}
+          BUILDNUMBER: ${{ github.run_number }}
+          GITSHA1: ${{ github.sha  }}
+        with:
+          registry: docker.pkg.github.com
+          name: ${{ github.repository_owner }}/${{ github.event.repository.name }}/ed
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+          tags: "${{ env.TAGS }}"
+          buildargs: BRANCH,BUILDNUMBER,GITSHA1
+          no_push: true
+
+      # this will publish to github container registry
+      - name: Publish to GitHub
+        if: github.event_name == 'push' && github.repository == env.MASTER_REPO
+        uses: elgohr/[email protected]
+        env:
+          BRANCH: ${{ env.GITHUB_BRANCH }}
+          BUILDNUMBER: ${{ github.run_number }}
+          GITSHA1: ${{ github.sha  }}
+        with:
+          registry: ghcr.io
+          name: ${{ github.repository_owner }}/ed
+          username: ${{ secrets.GHCR_USERNAME }}
+          password: ${{ secrets.GHCR_PASSWORD }}
+          tags: "${{ env.TAGS }}"
+          buildargs: BRANCH,BUILDNUMBER,GITSHA1
+
+      # this will publish to the pecan dockerhub repo
+      - name: Publish to Docker Hub
+        if: github.event_name == 'push' && github.repository == env.MASTER_REPO
+        uses: elgohr/[email protected]
+        env:
+          BRANCH: ${{ env.GITHUB_BRANCH }}
+          BUILDNUMBER: ${{ github.run_number }}
+          GITSHA1: ${{ github.sha  }}
+        with:
+          name: ${{ env.DOCKERHUB_ORG }}/ed
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_PASSWORD }}
+          tags: "${{ env.TAGS }}"
+          buildargs: BRANCH,BUILDNUMBER,GITSHA1

Dockerfile

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+# ----------------------------------------------------------------------
+# BUILD MODEL BINARY
+# ----------------------------------------------------------------------
+FROM debian:buster-slim AS builder
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION="2.2.0"
+ARG BINARY_VERSION="2.2"
+
+# specify fortran compiler
+ENV FC_TYPE=GNU
+
+# install dependencies
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       build-essential \
+       curl \
+       gfortran \
+       git \
+       libhdf5-dev \
+       libopenmpi-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# download, unzip and build ed2
+COPY . /src/
+WORKDIR /src/ED/build
+RUN ./install.sh -g -p docker && mv ed_*-opt ed
+
+########################################################################
+
+# ----------------------------------------------------------------------
+# BUILD PECAN FOR MODEL
+# ----------------------------------------------------------------------
+FROM debian:buster-slim
+
+# ----------------------------------------------------------------------
+# INSTALL MODEL SPECIFIC PIECES
+# ----------------------------------------------------------------------
+
+RUN apt-get update \
+    && apt-get install -y --no-install-recommends \
+       libhdf5-103 \
+       libopenmpi3 \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /data
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION="2.2.0"
+ENV MODEL_VERSION="${MODEL_VERSION}"
+
+# COPY model binary
+COPY --from=builder /src/ED/build/ed /usr/local/bin/ed
+
+

ED/build/make/include.mk.docker

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+#Makefile include include.mk.opt.ubuntu
+############################################################################
+
+# Define make (gnu make works best).
+MAKE=/usr/bin/make
+
+# libraries.
+BASE=$(ED_ROOT)/build/
+
+# HDF 5  Libraries
+USE_HDF5=1
+HDF5_INCS=-I/usr/include/hdf5/serial
+HDF5_LIBS=-L/usr/lib/x86_64-linux-gnu/hdf5/serial -lz -lhdf5_fortran -lhdf5 -lhdf5_hl
+#HDF5_INCS=-I/usr/include
+#HDF5_LIBS=-lz -lhdf5_fortran -lhdf5 -lhdf5_hl
+USE_COLLECTIVE_MPIO=0
+
+# netCDF libraries
+USENC=0
+NC_LIBS=-L/dev/null
+
+# interface
+USE_INTERF=1
+
+# MPI_Wtime
+USE_MPIWTIME=1
+
+# gfortran
+CMACH=PC_LINUX1
+F_COMP=mpif90
+F_OPTS=-O3 -ffree-line-length-none  -fno-whole-file
+C_COMP=mpicc
+C_OPTS=-O3
+LOADER=mpif90
+LOADER_OPTS=${F_OPTS}
+C_LOADER=mpicc
+LIBS=
+MOD_EXT=mod
+
+# using MPI libraries:
+MPI_PATH=
+PAR_INCS=
+PAR_LIBS=
+PAR_DEFS=-DRAMS_MPI
+
+# For IBM,HP,SGI,ALPHA,LINUX use these:
+ARCHIVE=ar rs