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Merge branch 'NOAA-GFDL:main' into main
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‎.github/workflows/Dockerfile.gnu‎

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#***********************************************************************
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#* GNU Lesser General Public License
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#*
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#* This file is part of the GFDL Flexible Modeling System (FMS).
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#*
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#* FMS is free software: you can redistribute it and/or modify it under
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#* the terms of the GNU Lesser General Public License as published by
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#* the Free Software Foundation, either version 3 of the License, or (at
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#* your option) any later version.
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#*
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#* FMS is distributed in the hope that it will be useful, but WITHOUT
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#* ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
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#* FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License
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#* for more details.
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#*
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#* You should have received a copy of the GNU Lesser General Public
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#* License along with FMS. If not, see <http://www.gnu.org/licenses/>.
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#***********************************************************************
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# FMS CI image recipefile for GNU
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# Runs on centos stream (builder has same base from redhat registry)
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#
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# arguments to specify versions to build can be given to docker or changed here (--build-arg name=val)
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FROM spack/rockylinux9:latest as builder
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ARG gcc_version=12.3.0
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ARG netcdfc_version=4.9.0
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ARG netcdff_version=4.6.0
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ARG libyaml_version=0.2.5
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ARG mpich_version=4.0.2
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COPY spack.env /opt/deps/spack.env
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# perl's download kept timing out
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RUN sed -i 's/connect_timeout: 10/connect_timeout: 600/' /opt/spack/etc/spack/defaults/config.yaml && \
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spack install gcc@${gcc_version} && \
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source /opt/spack/share/spack/setup-env.sh && \
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spack load gcc@${gcc_version} && \
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spack compiler find && \
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sed "s/COMPILER/gcc@$gcc_version/" /opt/deps/spack.env > spack.yaml && \
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sed -i "s/NETCDF_C_VERSION/$netcdfc_version/" spack.yaml && \
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sed -i "s/NETCDF_F_VERSION/$netcdff_version/" spack.yaml && \
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sed -i "s/LIBYAML_VERSION/$libyaml_version/" spack.yaml && \
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sed -i "s/MPI_LIB/mpich@$mpich_version/" spack.yaml && \
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spack env activate -d . && \
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spack -e . concretize -f > /opt/deps/deps.log && \
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spack install --fail-fast
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# copy built software to base from first image
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FROM rockylinux:9
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COPY --from=builder /opt/view/ /opt/view/
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COPY --from=builder /opt/deps/ /opt/deps/
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# input files used with --enable-input-tests
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# need to be on the dev boxes if building
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COPY ./fms_test_input /home/unit_tests_input
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RUN dnf install -y autoconf make automake m4 libtool pkg-config zip
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ENV FC="mpifort"
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ENV CC="mpicc"
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ENV MPICH_FC="/opt/view/bin/gfortran"
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ENV MPICH_CC="/opt/view/bin/gcc"
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ENV FCFLAGS="-I/opt/view/include"
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ENV CFLAGS="-I/opt/view/include"
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ENV LDFLAGS="-L/opt/view/lib"
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ENV LD_LIBRARY_PATH="/opt/view/lib:/opt/view/lib64:/usr/local/lib:/usr/local/lib64"
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ENV PATH="/opt/view/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin"

‎.github/workflows/build_ubuntu_gnu.yml‎

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‎.github/workflows/coupler.yml‎

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‎.github/workflows/github_autotools_gnu.yml‎

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# 'main' required ci, does a distcheck (builds, tests, check install)
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# image created off dockerfile in repo, compile/link flags are set there
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name: Build libFMS test with autotools
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on: [push, pull_request]
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# cancel running jobs if theres a newer push
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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conf-flag: [ --disable-openmp, --disable-setting-flags, --with-mpi=no, --disable-r8-defaults]
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input-flag: [--with-yaml, --enable-test-input=/home/unit_tests_input]
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exclude:
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- conf-flag: --with-mpi=no
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input-flag: --enable-test-input=/home/unit_tests_input
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container:
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image: noaagfdl/fms-ci-rocky-gnu:12.3.0
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env:
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TEST_VERBOSE: 1
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DISTCHECK_CONFIGURE_FLAGS: "${{ matrix.conf-flag }} ${{ matrix.input-flag }} ${{ matrix.io-flag }}"
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SKIP_TESTS: "test_yaml_parser.5" # temporary till fixes are in
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Prepare GNU autoconf for build
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run: autoreconf -if
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- name: Configure the build
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if: ${{ matrix.conf-flag != '--disable-setting-flags' }}
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run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} || cat config.log
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- name: Configure the build with compiler flags
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if: ${{ matrix.conf-flag == '--disable-setting-flags' }}
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run: ./configure ${DISTCHECK_CONFIGURE_FLAGS} FCFLAGS="-fdefault-real-8 -fdefault-double-8 -fcray-pointer -ffree-line-length-none -I/usr/include $FCFLAGS" || cat config.log
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- name: Build the library
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run: make distcheck
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if: ${{ matrix.conf-flag != '--with-mpi=no' }}
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- name: Build the library (without test suite for serial build)
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run: make
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if: ${{ matrix.conf-flag == '--with-mpi=no' }}

.github/workflows/intel_pr.yml renamed to .github/workflows/github_autotools_intel.yml

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on: pull_request
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# cancel running jobs if theres a newer push
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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intel-autotools:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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io-flag: ["--disable-deprecated-io", "--enable-deprecated-io"]
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container:
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image: intel/oneapi-hpckit:2022.2-devel-ubuntu20.04
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image: intel/oneapi-hpckit:2023.1.0-devel-ubuntu20.04
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env:
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CC: mpiicc
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FC: mpiifort
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CFLAGS: "-I/libs/include"
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FCFLAGS: "-I/libs/include -g -traceback"
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FCFLAGS: "-I/libs/include -g -traceback ${{ matrix.io-flag }}"
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LDFLAGS: "-L/libs/lib"
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TEST_VERBOSE: 1
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I_MPI_FABRICS: "shm" # needed for mpi in image
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path: /libs
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key: ${{ runner.os }}-intel-libs
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- name: Install packages for building
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run: apt update && apt install -y autoconf libtool automake zlibc zlib1g-dev
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run: apt-get update && apt-get install -y autoconf libtool automake zlibc zlib1g-dev
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- if: steps.cache.outputs.cache-hit != 'true'
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name: Build netcdf
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run: |
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./configure --prefix=/libs
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make -j install && cd
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- name: checkout
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Configure
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run: autoreconf -if ./configure.ac && ./configure --with-yaml
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- name: Compile
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run: make -j || make
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- name: Run test suite
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run: make check LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" SKIP_TESTS="$SKIP_TESTS" VERBOSE=1
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run: make check LD_LIBRARY_PATH="/libs/lib:$LD_LIBRARY_PATH" TEST_VERBOSE=1

.github/workflows/build_cmake_gnu.yml renamed to .github/workflows/github_cmake_gnu.yml

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on: [push, pull_request]
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# cancel running jobs if theres a newer push
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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omp-flags: [ -DOPENMP=on, -DOPENMP=off ]
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libyaml-flag: [ "", -DWITH_YAML=on ]
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io-flag: [ "", -DUSE_DEPRECATED_IO=on ]
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container:
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image: noaagfdl/hpc-me.ubuntu-minimal:cmake
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env:
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CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.libyaml-flag }} -D64BIT=on"
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CMAKE_FLAGS: "${{ matrix.omp-flags }} ${{ matrix.io-flag }} ${{ matrix.libyaml-flag }} -D64BIT=on"
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steps:
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- name: Checkout code
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Generate makefiles with CMake
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run: cmake $CMAKE_FLAGS .
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- name: Build the library

‎.github/workflows/github_coupler_gnu.yml‎

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name: Test coupler build
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on: [pull_request]
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# cancel running jobs if theres a newer push
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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coupler-build:
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runs-on: ubuntu-latest
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container:
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image: ghcr.io/noaa-gfdl/fms/fms-ci-rocky-gnu:12.3.0
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credentials:
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username: ${{ github.actor }}
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password: ${{ secrets.github_token }}
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env:
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CC: mpicc
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FC: mpif90
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CPPFLAGS: '-I/opt/view/include'
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FFLAGS: '-fallow-argument-mismatch' # mkmf uses FFLAGS instead of FC
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LDFLAGS: '-L/opt/view/lib'
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steps:
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- name: Checkout FMS
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uses: actions/checkout@v4
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with:
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path: FMS
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- name: Checkout FMScoupler
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uses: actions/checkout@v4
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with:
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repository: 'NOAA-GFDL/FMScoupler'
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path: FMScoupler
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- name: Test Null build
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run: FMScoupler/t/null_model_build.sh --local-fms

.github/workflows/update_docs.yml renamed to .github/workflows/github_doc_site.yml

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types: [published]
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workflow_dispatch:
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jobs:
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update_docs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Setup repo
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run: | # do autotool's job for substitutes since we don't need a full build environement
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mkdir gen_docs
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run: |
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sudo apt -y install doxygen graphviz
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doxygen gen_docs/Doxyfile
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- name: Deploy
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uses: peaceiris/actions-gh-pages@v3
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- name: Upload Pages Artifact
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uses: actions/upload-pages-artifact@v1
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./gen_docs/html
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path: 'gen_docs/html'
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deploy:
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needs: build
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# Grant GITHUB_TOKEN the permissions required to make a Pages deployment
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permissions:
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pages: write # to deploy to Pages
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id-token: write # to verify the deployment originates from an appropriate source
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# Deploy to the github-pages environment
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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# Specify runner + deployment step
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runs-on: ubuntu-latest
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v1

.github/workflows/lint_fms.yml renamed to .github/workflows/github_linter.yml

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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Run Lint
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uses: NOAA-GFDL/simple_lint@f5aa1fe976bd4c231db0536ba00cbfdc26708253
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with:

.github/workflows/am4_regression_parallelWorks_intel_tag.yml renamed to .github/workflows/parallelworks_am4_intel.yml

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