Bring main up to ngeet-2024

.github/workflows/docker-image.yml

@@ -1,4 +1,4 @@
-name: Docker image build
+name: Docker image build - base OS
 
 on:
   push:
@@ -10,44 +10,32 @@ on:
 jobs:
   build:
     runs-on: ubuntu-latest
-
+    strategy:
+      matrix:
+        platform: [linux/amd64, linux/arm64]
+
     steps:
     - name: checkout
       uses: actions/checkout@v4
+
+    - name: Docker QEMU
+      uses: docker/setup-qemu-action@v3
 
     - name: Docker Setup Buildx
       uses: docker/[email protected]
-      env: 
+      env:
           DOCKER_CONFIG: docker/baseos/gcc1120
-      #with:
-        # Buildx version. (eg. v0.3.0)
-        #version: # optional
-        # Sets the builder driver to be used
-        #driver: # optional, default is docker-container
-        # List of additional driver-specific options. (eg. image=moby/buildkit:master)
-        #driver-opts: # optional
-        # BuildKit daemon flags
-        #buildkitd-flags: # optional, default is --allow-insecure-entitlement security.insecure --allow-insecure-entitlement network.host
-        # BuildKit daemon config file
-        #buildkitd-config: # optional
-        # Inline BuildKit daemon config
-        #buildkitd-config-inline: # optional
-        # Sets up docker build command as an alias to docker buildx build
-        #install: # optional, default is false
-        # Switch to this builder instance
-        #use: # optional, default is true
-        # Optional address for docker socket or context from `docker context ls`
-        #endpoint: # optional
-        # Fixed platforms for current node. If not empty, values take priority over the detected ones
-        #platforms: # optional
-        # Append additional nodes to the builder
-        #append: # optional
-        # Cache buildx binary to GitHub Actions cache backend
-        #cache-binary: # optional, default is true
-        # Cleanup temp files and remove builder at the end of a job
-        #cleanup: # optional, default is true
-        # BuildKit daemon config file
-        #config: # optional
-        # Inline BuildKit daemon config
-        #config-inline: # optional
-
+
+    - name: Login to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Build and push
+      uses: docker/build-push-action@v6
+      with:
+        platform: ${{ matrix.platform }}
+        context: "{{defaultContext}}:docker/baseos/gcc1120"
+        push: true
+        tags: ngeetropics/baseos:testbuild-${{ matrix.platform}}

.gitignore

@@ -3,3 +3,16 @@
 *._*
 .DS_store
 .DS_Store
+
+# Documentation build
+/docs/build
+
+# docker
+.env
+
+# data
+*.nc
+*.cdl
+/docker/data/sites/met_data
+/docker/data/sites/bci_inventory_data
+/docker/data/sites/inventory_ctrl

docker/baseos/gcc1120/Dockerfile

@@ -0,0 +1,167 @@
+# ----------------------------------------------------------------------
+# Debian baseOS docker container to use with ELM/CTSM builds
+# AMD64 version
+# ----------------------------------------------------------------------
+
+FROM gcc:11.2.0
+LABEL maintainer.name="Gregory Lemieux" \
+      maintainer.email="[email protected]" \
+      author.name="Shawn P. Serbin" \
+      author.email="[email protected]" \
+      description="GCC-based image loaded with necessary dependencies for building HLM/HLM-FATES images"
+
+# Set a few variables that can be used to control the docker build
+# TODO: actually use these to allow for argument builds OR
+# remove if its not relevant
+ARG OPENMPI_VERSION=4.1.4
+ARG EXPAT_VERSION=2.4.7
+ARG HDF5_VERSION=1.12.2.3
+ARG NETCDF_VERSION=4.9.0.3
+ARG NETCDF_FORTRAN_VERSION=4.5.3
+
+# set path variables
+ENV PATH=/usr/local/bin:$PATH
+ENV LD_LIBRARY_PATH=/usr/local/lib64:$LD_LIBRARY_PATH
+ENV PATH=/usr/local/hdf5/bin:$PATH
+ENV PATH=/usr/local/netcdf/bin:$PATH
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/hdf5/lib
+ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/netcdf/lib
+ENV HDF5_DIR=/usr/local/hdf5
+
+# Update the system and install initial dependencies
+RUN apt-get update -y \
+    && apt-get install -y \
+    cmake \
+    git \
+    subversion \
+    bzip2 \
+    libgmp3-dev \
+    m4 \
+    wget \
+    libcurl4-openssl-dev \
+    zlib1g-dev \
+    libncurses5-dev \
+    libxml2 \
+    libxml2-dev \
+    csh \
+    liblapack-dev \
+    libblas-dev \
+    liblapack-dev \
+    libffi7 \
+    libffi-dev \
+    libxml-libxml-perl \
+    libxml2-utils \
+    vim \
+    libudunits2-0 \
+    libudunits2-dev \
+    udunits-bin \
+    python3 \
+    python3-dev \
+    python3-pip \
+    apt-utils \
+    ftp \
+    apt-transport-https \
+    libssl-dev \
+    openssl \
+    libncurses5-dev \
+    libsqlite3-dev \
+    gsl-bin \
+    libgsl-dev \
+    flex \
+    nco \
+    locales \
+    && rm -rf /var/lib/apt/lists/* \
+    && apt-get clean all
+
+## Install program to configure locales
+RUN dpkg-reconfigure locales && \
+  locale-gen C.UTF-8 && \
+    /usr/sbin/update-locale LANG=C.UTF-8
+RUN echo 'en_US.UTF-8 UTF-8' >> /etc/locale.gen && \
+      locale-gen
+## Set default locale for the environment
+ENV LC_ALL C.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US.UTF-8
+
+# ## check locales
+RUN locale -a
+
+# ## compile openMPI
+RUN cd / \
+    && wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-${OPENMPI_VERSION}.tar.gz \
+    && tar -zxvf openmpi-${OPENMPI_VERSION}.tar.gz \
+    && cd openmpi-${OPENMPI_VERSION} \
+    && export PATH=/usr/local/bin:$PATH \
+    && export LD_LIBRARY_PATH=/usr/local/lib64:$LD_LIBRARY_PATH \
+    && ./configure --enable-static \
+    && make \
+    && make install \
+    && cd / \
+    && rm -r openmpi-${OPENMPI_VERSION} \
+    && rm openmpi-${OPENMPI_VERSION}.tar.gz \
+    && ldconfig
+
+## Compile Expat XML parser
+RUN cd / \
+    && wget https://github.com/libexpat/libexpat/releases/download/R_2_4_7/expat-2.4.7.tar.bz2 \
+    && tar -xvjf expat-2.4.7.tar.bz2 \
+    && cd expat-2.4.7 \
+    && ./configure \
+    && make \
+    && make install \
+    && cd / \
+    && rm -r expat-2.4.7 \
+    && rm expat-2.4.7.tar.bz2
+
+## HDF5 - use alternative source since main HDF5 source doesnt have useful download links
+#https://support.hdfgroup.org/ftp/HDF5/releases/
+RUN cd / \
+    && mkdir -p /usr/local/hdf5 \
+    && wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.1/src/hdf5-1.12.1.tar.gz \
+    && tar -zxvf hdf5-1.12.1.tar.gz \
+    && cd hdf5-1.12.1 \
+    && CC=mpicc ./configure --enable-fortran --enable-parallel --prefix=/usr/local/hdf5 \
+    && make \
+    && make install \
+    && export PATH=/usr/local/hdf5/bin:$PATH \
+    && export LD_LIBRARY_PATH=/usr/local/hdf5/lib/libhdf5 \
+    && cd / \
+    && rm -r hdf5-1.12.1 \
+    && rm hdf5-1.12.1.tar.gz
+
+## netCDF & netCDF-Fortran
+RUN cd / \
+    && mkdir -p /usr/local/netcdf \
+    && wget https://downloads.unidata.ucar.edu/netcdf-c/4.8.1/netcdf-c-4.8.1.tar.gz \
+    && tar -zxvf netcdf-c-4.8.1.tar.gz \
+    && cd netcdf-c-4.8.1 \
+    && export H5DIR=/usr/local/hdf5 \
+    && export NCDIR=/usr/local/netcdf \
+    && CC=mpicc CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib ./configure --enable-parallel-tests --prefix=${NCDIR} \
+    && make \
+    && make install \
+    && export PATH=/usr/local/netcdf/bin:$PATH \
+    && export LD_LIBRARY_PATH=/usr/local/netcdf/lib \
+    && cd / \
+    && rm -r netcdf-c-4.8.1 \
+    && rm netcdf-c-4.8.1.tar.gz \
+    && wget https://downloads.unidata.ucar.edu/netcdf-fortran/4.5.4/netcdf-fortran-4.5.4.tar.gz \
+    && tar -zxvf netcdf-fortran-4.5.4.tar.gz \
+    && cd netcdf-fortran-4.5.4 \
+    && export NCDIR=/usr/local/netcdf \
+    && export NFDIR=/usr/local/netcdf \
+    && FC=mpif90 CPPFLAGS=-I${NCDIR}/include LDFLAGS=-L${NCDIR}/lib ./configure --prefix=${NFDIR} --enable-parallel-tests \
+    && make \
+    && make install \
+    && cd / \
+    && rm -r netcdf-fortran-4.5.4 \
+    && rm netcdf-fortran-4.5.4.tar.gz
+
+# This is the minimum version of scipy to avoid fates#1242
+ RUN pip3 install 'scipy==1.11.4' 'netCDF4==1.7.1'
+
+# Add symlink to python3 to alias python
+RUN ln -sf /usr/bin/python3 /usr/bin/python
+
+### EOF