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Add generic scripts to aid in building the prognostic run environment (#2035)
* Generalize install script for ESMF * Generalze install script for FMS * Generalize install script for NCEPlibs * Tag base image as 1.0.1 * Add script to install the fortran model * Add script for installation of fv3net Python dependencies * Add script for installing the Python wrapper * Add script to install call_py_fort * Parametrize local packages for fv3net install script
1 parent 2465a08 commit 61c6fe0

13 files changed

+141
-98
lines changed

‎.environment-scripts/install_call_py_fort.sh

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#!/bin/bash
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set -e
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PREFIX=$1
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URL=https://github.com/nbren12/call_py_fort.git
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BRANCH=v0.2.0
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git clone $URL --branch=$BRANCH $PREFIX
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cd $PREFIX
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make
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make install
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ldconfig

‎.environment-scripts/install_esmf.sh

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#!/bin/bash
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set -e
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CLONE_PREFIX=$1
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INSTALL_PREFIX=$2
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ESMF_OS=$3
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ESMF_COMPILER=$4
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ESMF_SITE=$5
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NETCDF_INCLUDE=$6
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export ESMF_DIR=$CLONE_PREFIX
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export ESMF_INSTALL_PREFIX=$INSTALL_PREFIX
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export ESMF_INSTALL_MODDIR=$ESMF_INSTALL_PREFIX/include
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export ESMF_INSTALL_HEADERDIR=$ESMF_INSTALL_PREFIX/include
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export ESMF_INSTALL_LIBDIR=$ESMF_INSTALL_PREFIX/lib
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export ESMF_INSTALL_BINDIR=$ESMF_INSTALL_PREFIX/bin
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export ESMF_NETCDF_INCLUDE=$NETCDF_INCLUDE
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export ESMF_NETCDF_LIBS="-lnetcdf -lnetcdff"
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export ESMF_BOPT=O3
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# These flags set how the build is configured depending on the platform:
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# https://github.com/esmf-org/esmf/tree/develop/build_config
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export ESMF_OS=$ESMF_OS
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export ESMF_COMPILER=$ESMF_COMPILER
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export ESMF_SITE=$ESMF_SITE
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# We may want to upgrade to ESMF_8_1_0 to make things easier on other platforms.
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git clone -b ESMF_8_0_0 --depth 1 https://github.com/esmf-org/esmf.git $ESMF_DIR
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cd $ESMF_DIR
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make lib -j24
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make install
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make installcheck

‎.environment-scripts/install_fms.sh

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#!/bin/bash
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set -e
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INSTALL_PREFIX=$1
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cd $INSTALL_PREFIX
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autoreconf -f --install
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./configure
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make -j8
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mv $INSTALL_PREFIX/*/*.o $INSTALL_PREFIX/*/*.h $INSTALL_PREFIX/*/*.mod $INSTALL_PREFIX/

‎.environment-scripts/install_fv3gfs_fortran.sh

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#!/bin/bash
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set -e
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PREFIX=$1
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PLATFORM=$2
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INSTALL_PREFIX=$3
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cd $PREFIX
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./configure $PLATFORM
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make -j 8
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PREFIX=$INSTALL_PREFIX make install

‎.environment-scripts/install_fv3net_python_dependencies.sh

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#!/bin/bash
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set -e
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REQUIREMENTS_PATH=$1
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LOCAL_DEPENDENCIES=${@:2}
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pip install --no-cache-dir -r $REQUIREMENTS_PATH
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for dependency in $LOCAL_DEPENDENCIES
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do
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pip install --no-cache-dir --no-dependencies -e $dependency
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done

‎.environment-scripts/install_nceplibs.sh

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#!/bin/bash
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set -e
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CLONE_PREFIX=$1
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INSTALL_PREFIX=$2
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PLATFORM=$3
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COMPILER=$4
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URL=https://github.com/NCAR/NCEPlibs.git
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SHA=3da51e139d5cd731c9fc27f39d88cb4e1328212b
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git clone $URL $CLONE_PREFIX
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cd $CLONE_PREFIX
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git checkout $SHA
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mkdir -p $INSTALL_PREFIX
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echo "y" | bash make_ncep_libs.sh -s $PLATFORM -c $COMPILER -d $INSTALL_PREFIX -o 1

‎.environment-scripts/install_python_wrapper.sh

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#!/bin/bash
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set -e
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FV3_DIR=$1
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make -C $FV3_DIR wrapper_build
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pip install --no-dependencies $FV3_DIR/wrapper/dist/*.whl

‎Makefile

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@@ -11,7 +11,7 @@ CACHE_TAG =latest
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BEAM_VERSION = 2.37.0
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UBUNTU_IMAGE = ubuntu@sha256:9101220a875cee98b016668342c489ff0674f247f6ca20dfc91b91c0f28581ae
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# prognostic base image is updated manually, not on every commit
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PROGNOSTIC_BASE_VERSION = 1.0.0
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PROGNOSTIC_BASE_VERSION = 1.0.1
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DOCKER_INTERACTIVE_ARGS = \
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--tty \
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--interactive \

‎docker/prognostic_run/Dockerfile

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@@ -4,44 +4,39 @@ FROM ${BASE_IMAGE} as bld
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# build/install the fortran model
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COPY external/fv3gfs-fortran/ /tmp/fortran-build
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RUN cd /tmp/fortran-build/FV3 && \
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./configure gnu_docker && \
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sed -i "33i CALLPYFORT=Y" conf/configure.fv3 && \
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make -j 8 && \
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PREFIX=/usr/local make install
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# Python Stuff Here
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#
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# Equivalent to passing --no-cache-dir to every pip install
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ENV PIP_NO_CACHE_DIR=off
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# Install dependencies
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COPY docker/prognostic_run/requirements.txt /tmp/requirements.txt
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RUN pip install -r /tmp/requirements.txt
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# compile and install the wrapper. Then import fv3gfs.wrapper as a minimal test
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# that it works.
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RUN make -C /tmp/fortran-build/FV3 wrapper_build &&\
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pip3 install --no-dependencies /tmp/fortran-build/FV3/wrapper/dist/*.whl && \
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python3 -c 'import fv3gfs.wrapper'
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COPY .environment-scripts/install_fv3gfs_fortran.sh .
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RUN CALLPYFORT=Y bash install_fv3gfs_fortran.sh /tmp/fortran-build/FV3 gnu_docker /usr/local
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# Install the Python dependencies
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COPY docker/prognostic_run/requirements.txt /fv3net/docker/prognostic_run/requirements.txt
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COPY external/vcm /fv3net/external/vcm
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RUN pip3 install --no-dependencies -e /fv3net/external/vcm
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COPY external/artifacts /fv3net/external/artifacts
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RUN pip3 install --no-dependencies -e /fv3net/external/artifacts
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COPY external/loaders /fv3net/external/loaders
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RUN pip3 install --no-dependencies -e /fv3net/external/loaders
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COPY external/fv3fit /fv3net/external/fv3fit
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RUN pip3 install --no-dependencies -e /fv3net/external/fv3fit
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COPY external/fv3kube /fv3net/external/fv3kube
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RUN pip3 install --no-dependencies -e /fv3net/external/fv3kube
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COPY workflows/post_process_run /fv3net/workflows/post_process_run
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RUN pip3 install --no-dependencies -e /fv3net/workflows/post_process_run
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COPY workflows/prognostic_c48_run/ /fv3net/workflows/prognostic_c48_run
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COPY external/emulation /fv3net/external/emulation
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COPY external/radiation /fv3net/external/radiation
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COPY .environment-scripts/install_fv3net_python_dependencies.sh .
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RUN bash install_fv3net_python_dependencies.sh \
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/fv3net/docker/prognostic_run/requirements.txt \
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/fv3net/external/vcm \
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/fv3net/external/artifacts \
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/fv3net/external/loaders \
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/fv3net/external/fv3fit \
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/fv3net/external/fv3kube \
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/fv3net/workflows/post_process_run \
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/fv3net/workflows/prognostic_c48_run \
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/fv3net/external/emulation \
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/fv3net/external/radiation
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# compile and install the wrapper. Then import fv3gfs.wrapper as a minimal test
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# that it works.
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COPY .environment-scripts/install_python_wrapper.sh .
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RUN CALLPYFORT=Y bash install_python_wrapper.sh /tmp/fortran-build/FV3
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RUN python3 -c 'import fv3gfs.wrapper'
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RUN echo "ulimit -s unlimited" >> /etc/bash.bashrc && \
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mkdir /outdir && \
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ENV LC_ALL=C.UTF-8
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ENV LANG=C.UTF-8
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COPY workflows/prognostic_c48_run/ /fv3net/workflows/prognostic_c48_run
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RUN pip install --no-dependencies -e /fv3net/workflows/prognostic_c48_run
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# Override microphysics emulation
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COPY external/emulation /fv3net/external/emulation
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RUN pip install --no-dependencies -e /fv3net/external/emulation
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ENV VAR_META_PATH=/fv3net/external/emulation/microphysics_parameter_metadata.yaml
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ENV OUTPUT_FREQ_SEC=18000
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RUN chmod +x /fv3net/projects/microphysics/scripts/*
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ENV PATH=/fv3net/projects/microphysics/scripts:${PATH}
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# Add python radiation port
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COPY external/radiation /fv3net/external/radiation
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RUN pip install --no-dependencies -e /fv3net/external/radiation
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ENV PYTHONPATH=/fv3net/workflows/prognostic_c48_run:/fv3net/external/fv3fit:/fv3net/external/emulation:/fv3net/external/vcm:/fv3net/external/artifacts:/fv3net/external/loaders:/fv3net/external/fv3kube:/fv3net/workflows/post_process_run:/fv3net/external/radiation:${PYTHONPATH}
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WORKDIR /fv3net/workflows/prognostic_c48_run
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CMD ["bash"]

‎docker/prognostic_run/base.Dockerfile

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rsync \
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wget
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COPY docker/prognostic_run/scripts/install_esmf.sh install_esmf.sh
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RUN bash install_esmf.sh /usr/local/esmf
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COPY .environment-scripts/install_esmf.sh .
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RUN bash install_esmf.sh /esmf /usr/local/esmf Linux gfortran default
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COPY docker/prognostic_run/scripts/install_fms.sh install_fms.sh
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COPY .environment-scripts/install_fms.sh .
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COPY external/fv3gfs-fortran/FMS /FMS
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RUN bash install_fms.sh /FMS
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RUN CC=/usr/bin/mpicc \
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FC=/usr/bin/mpif90 \
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LDFLAGS='-L/usr/lib' \
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LOG_DRIVER_FLAGS='--comments' \
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CPPFLAGS='-I/usr/include -Duse_LARGEFILE -DMAXFIELDMETHODS_=500 -DGFS_PHYS' \
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FCFLAGS='-fcray-pointer -Waliasing -ffree-line-length-none -fno-range-check -fdefault-real-8 -fdefault-double-8 -fopenmp' \
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bash install_fms.sh /FMS
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COPY docker/prognostic_run/scripts/install_nceplibs.sh .
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RUN bash install_nceplibs.sh /opt/NCEPlibs
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COPY .environment-scripts/install_nceplibs.sh .
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RUN bash install_nceplibs.sh /NCEPlibs /opt/NCEPlibs linux gnu
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ENV ESMF_DIR=/usr/local/esmf
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ENV CALLPY_DIR=/usr/local
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ENV FMS_DIR=/FMS
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ENV FV3GFS_FORTRAN_DIR=/external/fv3gfs-fortran
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ENV ESMF_INC="-I${ESMF_DIR}/include -I${ESMF_DIR}/mod/modO3/Linux.gfortran.64.mpiuni.default/"
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ENV ESMF_INC="-I${ESMF_DIR}/include"
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ENV FMS_LIB=${FMS_DIR}/libFMS/.libs/
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ENV ESMF_LIB=${ESMF_DIR}/lib
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ENV CALLPYFORT_LIB=${CALLPY_DIR}/lib
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ENV CALLPYFORT_INCL=${CALLPY_DIR}/include
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ENV LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${ESMF_LIB}:${FMS_LIB}:${CALLPYFORT_LIB}
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RUN cd /opt && git clone https://github.com/nbren12/call_py_fort.git --branch=v0.2.0
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ENV CALLPY=/opt/call_py_fort \
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PYTHONPATH=${CALLPY}/src/:$PYTHONPATH
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RUN cd ${CALLPY} && make && make install && ldconfig
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COPY .environment-scripts/install_call_py_fort.sh .
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RUN bash install_call_py_fort.sh $CALLPY
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# Install gcloud
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RUN apt-get update && apt-get install -y apt-transport-https ca-certificates gnupg curl gettext && \

‎docker/prognostic_run/scripts/install_esmf.sh

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‎docker/prognostic_run/scripts/install_fms.sh

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‎docker/prognostic_run/scripts/install_nceplibs.sh

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