Build FATES container for PEcAn and create job.sh to run fates in the container

models/fates/Dockerfile

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+# this needs to be at the top, what version are we building
+ARG IMAGE_VERSION="latest"
+
+# ----------------------------------------------------------------------
+# BUILD MODEL
+# ----------------------------------------------------------------------
+FROM pecan/models:${IMAGE_VERSION}
+
+# load packages before adding CTSM
+RUN apt update && apt upgrade -y
+RUN apt install -y \
+    sudo \
+    build-essential \
+    python3-dev \
+    cmake \
+    gfortran-9 \
+    zlib1g-dev \
+    byacc \
+    libblas-dev \
+    liblapack-dev \
+    libxml2-utils \
+    libxml-libxml-perl \
+    libgdal-dev \
+    xmlstarlet \
+    csh \
+    diffutils \
+    rsync
+
+RUN update-alternatives --install /usr/bin/gfortran gfortran /usr/bin/gfortran-9 100
+
+RUN echo '/usr/local/lib' > /etc/ld.so.conf.d/local.conf && ldconfig
+
+WORKDIR /tmp/sources
+
+RUN wget -q http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz && \
+    tar zxf mpich-3.3.2.tar.gz && \
+    cd mpich-3.3.2 && \
+    ./configure --prefix=/usr/local && \
+    make -j 2 install
+
+RUN  wget -q https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.0/src/hdf5-1.12.0.tar.gz && \
+     tar zxf hdf5-1.12.0.tar.gz && \
+     cd hdf5-1.12.0 && \
+     ./configure --prefix=/usr/local && \
+     make -j 2 install
+
+RUN  wget -q https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.7.4.tar.gz && \
+     tar zxf v4.7.4.tar.gz && \
+     cd netcdf-c-4.7.4 && \
+     ./configure --prefix=/usr/local && \
+     make -j 2 install && \
+     ldconfig
+
+RUN  wget -q https://github.com/Unidata/netcdf-fortran/archive/refs/tags/v4.5.3.tar.gz && \
+     tar zxf v4.5.3.tar.gz && \
+     cd netcdf-fortran-4.5.3 && \
+     ## original netcdf(version=4.7.3): /usr,  ; fates netcdf(version>=4.7.4): /usr/local; --enable-fortran to ensure netcdf.mod
+     ./configure --prefix=/usr/local LDFLAGS="-L/usr/local/lib" CPPFLAGS="-I/usr/local/include" --enable-fortran && \ 
+     make -j 2 install && \
+     ldconfig
+
+RUN  wget -q https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz && \
+     tar zxf pnetcdf-1.12.1.tar.gz && \
+     cd pnetcdf-1.12.1 && \
+     ./configure MPIF77=/usr/local/bin/mpif77 MPIF90=/usr/local/bin/mpif90 MPICXX=/usr/local/bin/mpicxx MPICC=/usr/local/bin/mpicc && \
+     make -j 2 install && \
+     ldconfig
+
+RUN cd  /tmp/sources \
+    wget -q https://github.com/esmf-org/esmf/archive/refs/tags/ESMF_8_2_0.tar.gz && \
+    tar zxf ESMF_8_2_0.tar.gz && \
+    cd esmf-ESMF_8_2_0 && \
+    export ESMF_DIR='/tmp/sources/esmf-ESMF_8_2_0' && \
+    export ESMF_INSTALL_PREFIX='/usr/local' && \
+    export ESMF_LAPACK="netlib" && \
+    export ESMF_LAPACK_LIBS="-llapack -lblas" && \
+    export ESMF_LAPACK_LIBPATH="/usr/lib/x86_64-linux-gnu" && \
+    export ESMF_NETCDF="nc-config" && \
+    make && \
+    make install && \
+    ldconfig
+
+RUN rm -rf /tmp/sources
+RUN pip install --upgrade pip setuptools
+
+## Above has been tested in the pecan/model container
+
+########################################################################
+
+## Below needs further discussion.
+
+## Load CTSM from https://github.com/NorESMhub/noresm-land-sites-platform/blob/main/docker/api/entrypoint_api.sh
+## Following the structure of ED, download CTSM
+WORKDIR /src
+RUN git clone https://github.com/ESCOMP/CTSM.git && \
+    ## go to model folder
+    cd CTSM && \
+    ## Checkout specific CTSM version, which has been tested in the container, more recent version than this needs to be tested in the future.
+    git checkout ctsm5.1.dev108 && \ 
+    ## Download fates (tag = sci.1.58.1_api.24.1.0), the version can be modified in Externals_CLM.cfg & CISM should be manually cloned
+    ./manage_externals/checkout_externals
+
+RUN set -e && \
+    ## set home folder for running CTSM-fates.
+    USER=root && \
+    HOME=/root && \
+    ## create .bashrc file for setting basic compiling parameters for CTSM-fates
+    export USER="$USER" && \
+    ## 1 /usr/bin/python3
+    export PYTHONPATH='/usr/bin/python3' && \ 
+    export CIME_MACHINE=container && \
+    export MPICC=mpicc && \
+    export MPIFC=mpif90 && \
+    export MPIF90=mpif90 && \
+    export MPIF77=mpif77 && \
+    ## if CESMDATAROOT is changed, also change in config.py and other relevant places.
+    ## 2 /src/data
+    export CESMDATAROOT=${CESMDATAROOT:-/src/data} && \ 
+    ## Copy dotcime ((https://github.com/NorESMhub/ctsm-api/tree/main/docker/dotcime)) to pecan/models/fates folder
+    ## Dotcime is a key file for setting the compiling environment for CTSM-fates, SHOULD be kept in the home directory of the fates model conatiner as '.cime'
+    cd .. && \
+    git clone https://github.com/NorESMhub/ctsm-api.git && \
+    cp -r ./ctsm-api/docker/dotcime "$HOME"/.cime && \
+    rm -rf /src/ctsm-api
+
+
+########################################################################
+
+# Some variables that can be used to set control the docker build
+ARG MODEL_VERSION=git
+ENV MODEL_VERSION=${MODEL_VERSION}
+
+# Setup model_info file
+## model.json 
+COPY model_info.json /work/model.json
+RUN sed -i -e "s/@VERSION@/${MODEL_VERSION}/g" \
+           -e "s#@BINARY@#/usr/local/bin/fates.${MODEL_VERSION}#g" /work/model.json