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Merge branch 'hotfix/0.41.1'
* hotfix/0.41.1: Version 0.41.1 GHA: Run ci for ci branch Add GHA build-hpc running on ECMWF GPU partition GHA build: Add open-mpi version to CACHE_SUFFIX for macos to prevent failures with homebrew upgrades GHA build: Skip atlas_test_omp_sort for nvhpc 25.1 (problem in Release build only) GHA build: Update action (using github-hosted-runners) Fix warnings for hic Fix warnings for atlas_io Add cmake option to SKIP_TEST_atlas_test_omp_sort Add SKIP_TEST_<test-name> for atlas_test_field_foreach and atlas_test_array_foreach Add cmake option WARNING_AS_ERROR to add -Werror as CXX flag Filter tests with MPI 4 and MPI_SLOTS Extend macros to suppress warnings based on pragmas Fix assemble_global_matrix with ATLAS_BITS_LOCAL=64 Fix compilation with ATLAS_BITS_LOCAL=64 Fix RegionalLinear2D interpolation with ATLAS_BITS_LOCAL=64 atlas-docs: Build doxygen from source
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‎.github/docs-config.yml‎

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# note: each step is executed in own process
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build-steps:
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- git clone --depth 1 https://github.com/ecmwf/atlas-docs.git $RUNNER_TEMP/atlas-docs
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- sudo apt install -y -q doxygen texlive-full
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- |
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wget https://github.com/doxygen/doxygen/archive/refs/tags/Release_1_13_2.tar.gz
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tar xzf Release_1_13_2.tar.gz
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cmake -S doxygen-Release_1_13_2 -B doxygen
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cmake --build doxygen -j16
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sudo cmake --install doxygen
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- sudo apt install -y -q ghostscript texlive-full
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- |
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cd $RUNNER_TEMP/atlas-docs
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make PUBLIC=1 WITH_ECKIT=1 WITH_DOXYGEN=1 ATLAS_SOURCE_DIR=$GITHUB_WORKSPACE clean html

‎.github/workflows/build-hpc.yml‎

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name: build-hpc
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# Controls when the action will run
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on:
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# Trigger the workflow on all pushes to main and develop, except on tag creation
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push:
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branches:
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- main
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- develop
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- ci
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tags-ignore:
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- '**'
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# Trigger the workflow on all pull requests
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pull_request: ~
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# Allow workflow to be dispatched on demand
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workflow_dispatch: ~
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# Trigger after public PR approved for CI
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pull_request_target:
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types: [labeled]
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env:
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ATLAS_TOOLS: ${{ github.workspace }}/tools
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CTEST_PARALLEL_LEVEL: 1
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CACHE_SUFFIX: v1 # Increase to force new cache to be created
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jobs:
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ci-hpc:
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name: ci-hpc
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if: ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}
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strategy:
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fail-fast: false # false: try to complete all jobs
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matrix:
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name:
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- ac-gpu nvhpc
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include:
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- name: ac-gpu nvhpc
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site: ac-batch
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troika_user_secret: HPC_CI_GPU_SSH_USER
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sbatch_options: |
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#SBATCH --time=00:20:00
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#SBATCH --nodes=1
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#SBATCH --ntasks=4
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#SBATCH --cpus-per-task=32
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#SBATCH --gpus-per-task=1
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#SBATCH --mem=200G
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#SBATCH --qos=dg
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modules:
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- cmake
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- ninja
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- prgenv/nvidia
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- hpcx-openmpi/2.14.0-cuda
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- fftw
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- qhull
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- eigen
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cmake_options: -DMPI_SLOTS=4 -DENABLE_WARNING_AS_ERROR=ON
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runs-on: [self-hosted, linux, hpc]
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env:
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GH_TOKEN: ${{ github.token }}
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steps:
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- uses: ecmwf-actions/reusable-workflows/ci-hpc-generic@v2
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with:
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site: ${{ matrix.site }}
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troika_user: ${{ secrets[matrix.troika_user_secret] }}
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sbatch_options: ${{ matrix.sbatch_options }}
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output_dir: ${{ matrix.output_dir || '' }}
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workdir: ${{ matrix.workdir || '' }}
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template_data: |
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cmake_options:
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- -DENABLE_MPI=ON
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- -DENABLE_ACC=ON
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- -DENABLE_CUDA=ON
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- -DSKIP_TEST_atlas_test_field_foreach=TRUE
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- ${{ matrix.cmake_options || '' }}
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ctest_options: ${{ matrix.ctest_options || '' }}
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dependencies:
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ecmwf/ecbuild:
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version: develop
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ecmwf/eckit:
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version: develop
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cmake_options:
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- -DENABLE_MPI=ON
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- -DENABLE_CUDA=OFF
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- -DENABLE_TESTS=OFF
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- -DENABLE_ECKIT_SQL=OFF
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- -DENABLE_ECKIT_CMD=OFF
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- -DENABLE_AIO=OFF
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- -DENABLE_WARNINGS=OFF
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- ${{ matrix.cmake_options || '' }}
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ecmwf/fckit:
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version: develop
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cmake_options:
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- -DENABLE_TESTS=OFF
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- ${{ matrix.cmake_options || '' }}
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ecmwf-ifs/fiat:
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version: develop
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cmake_options:
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- -DENABLE_MPI=ON
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- -DENABLE_TESTS=OFF
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- ${{ matrix.cmake_options || '' }}
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ecmwf-ifs/ectrans:
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version: develop
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cmake_options:
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- -DENABLE_MPI=ON
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- -DENABLE_ACC=ON
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- -DENABLE_GPU=ON
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- -DENABLE_TESTS=OFF
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- ${{ matrix.cmake_options || '' }}
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template: |
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set +x
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module_load() {
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echo "+ module load $1"
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module load $1
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}
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{% for module in "${{ join(matrix.modules, ',') }}".split(',') %}
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module_load {{module}}
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{% endfor %}
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echo "+ module list"
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module list
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BASEDIR=$PWD
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export CMAKE_TEST_LAUNCHER="srun;-n;1"
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export CMAKE_PREFIX_PATH=$BASEDIR/install:$CMAKE_PREFIX_PATH
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{% for repo_name, options in dependencies.items() %}
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name=$(basename {{repo_name}})
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echo "::group::Get dependency $name"
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echo "+ mkdir -p $name"
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mkdir -p $name
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echo "+ pushd $name"
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pushd $name
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echo "+ git init"
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git init
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echo "+ git remote add origin ${{ github.server_url }}/{{repo_name}}"
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git remote add origin ${{ github.server_url }}/{{repo_name}}
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echo "+ git fetch origin {{options['version']}}"
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git fetch origin {{options['version']}}
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echo "+ git reset --hard FETCH_HEAD"
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git reset --hard FETCH_HEAD
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echo "+ cmake -G Ninja -S . -B build {{ options['cmake_options']|join(' ') }}"
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cmake -G Ninja -S . -B build {{ options['cmake_options']|join(' ') }}
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start=`date +%s`
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echo "+ cmake --build build"
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cmake --build build
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end=`date +%s`
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runtime=$((end-start))
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echo "Build $name took $runtime seconds"
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echo "+ cmake --install build --prefix \$BASEDIR/install/$name"
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cmake --install build --prefix $BASEDIR/install/$name
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echo "+ export PATH=\$BASEDIR/install/$name/bin:\$PATH"
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export PATH=$BASEDIR/install/$name/bin:$PATH
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echo "+ popd"
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popd
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echo "::endgroup::"
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{% endfor %}
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REPO=${{ github.event.pull_request.head.repo.full_name || github.repository }}
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SHA=${{ github.event.pull_request.head.sha || github.sha }}
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name=$(basename $REPO)
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echo "::group::Checkout $name"
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echo "+ mkdir -p $name"
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mkdir -p $name
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echo "+ pushd $name"
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pushd $name
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echo "+ git init"
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git init
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echo "+ git remote add origin ${{ github.server_url }}/$REPO"
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git remote add origin ${{ github.server_url }}/$REPO
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echo "+ git fetch origin $SHA"
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git fetch origin $SHA
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echo "+git reset --hard FETCH_HEAD"
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git reset --hard FETCH_HEAD
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echo "+ popd"
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popd
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echo "::endgroup::"
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echo "::group::Build $name"
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echo "+ cmake -G Ninja -S $name -B build {{ cmake_options|join(' ') }}"
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cmake -G Ninja -S $name -B build {{ cmake_options|join(' ') }}
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start=`date +%s`
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echo "+ cmake --build build"
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cmake --build build
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end=`date +%s`
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runtime=$((end-start))
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echo "Build $name took $runtime seconds"
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echo "::endgroup::"
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echo "::group::Test $name"
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export ATLAS_FINALISES_MPI=1
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echo "+ ctest --test-dir build --output-on-failure {{ ctest_options }}"
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ctest --test-dir build --output-on-failure {{ ctest_options }}
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echo "::endgroup::"
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echo "::group::Install $name"
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echo "+ cmake --install build --prefix $BASEDIR/install/$name"
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cmake --install build --prefix $BASEDIR/install/$name
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echo "+ export PATH=\$BASEDIR/install/$name/bin:\$PATH"
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export PATH=$BASEDIR/install/$name/bin:$PATH
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echo "::endgroup::"
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echo "::group::Verify $name installation"
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echo "+ atlas --info"
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atlas --info
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echo "::endgroup::"
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echo "::group::Cleanup"
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set -x
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rm -r $name
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rm -r build
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rm -r $BASEDIR/install
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{% for repo_name in dependencies.keys() %}
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name=$(basename {{repo_name}})
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rm -r $name
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{% endfor %}
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echo "::endgroup::"
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set +x

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