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* 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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@wdeconinck
wdeconinck committed Feb 18, 2025
2 parents afcdc8d + 360f43c commit a50e28f
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8 changes: 7 additions & 1 deletion .github/docs-config.yml
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# note: each step is executed in own process
build-steps:
- git clone --depth 1 https://github.com/ecmwf/atlas-docs.git $RUNNER_TEMP/atlas-docs
- sudo apt install -y -q doxygen texlive-full
- |
wget https://github.com/doxygen/doxygen/archive/refs/tags/Release_1_13_2.tar.gz
tar xzf Release_1_13_2.tar.gz
cmake -S doxygen-Release_1_13_2 -B doxygen
cmake --build doxygen -j16
sudo cmake --install doxygen
- sudo apt install -y -q ghostscript texlive-full
- |
cd $RUNNER_TEMP/atlas-docs
make PUBLIC=1 WITH_ECKIT=1 WITH_DOXYGEN=1 ATLAS_SOURCE_DIR=$GITHUB_WORKSPACE clean html
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222 changes: 222 additions & 0 deletions .github/workflows/build-hpc.yml
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name: build-hpc

# Controls when the action will run
on:

# Trigger the workflow on all pushes to main and develop, except on tag creation
push:
branches:
- main
- develop
- ci
tags-ignore:
- '**'

# Trigger the workflow on all pull requests
pull_request: ~

# Allow workflow to be dispatched on demand
workflow_dispatch: ~

# Trigger after public PR approved for CI
pull_request_target:
types: [labeled]

env:
ATLAS_TOOLS: ${{ github.workspace }}/tools
CTEST_PARALLEL_LEVEL: 1
CACHE_SUFFIX: v1 # Increase to force new cache to be created

jobs:
ci-hpc:
name: ci-hpc
if: ${{ !github.event.pull_request.head.repo.fork && github.event.action != 'labeled' || github.event.label.name == 'approved-for-ci' }}

strategy:
fail-fast: false # false: try to complete all jobs

matrix:
name:
- ac-gpu nvhpc

include:
- name: ac-gpu nvhpc
site: ac-batch
troika_user_secret: HPC_CI_GPU_SSH_USER
sbatch_options: |
#SBATCH --time=00:20:00
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --cpus-per-task=32
#SBATCH --gpus-per-task=1
#SBATCH --mem=200G
#SBATCH --qos=dg
modules:
- cmake
- ninja
- prgenv/nvidia
- hpcx-openmpi/2.14.0-cuda
- fftw
- qhull
- eigen
cmake_options: -DMPI_SLOTS=4 -DENABLE_WARNING_AS_ERROR=ON

runs-on: [self-hosted, linux, hpc]
env:
GH_TOKEN: ${{ github.token }}
steps:
- uses: ecmwf-actions/reusable-workflows/ci-hpc-generic@v2
with:
site: ${{ matrix.site }}
troika_user: ${{ secrets[matrix.troika_user_secret] }}
sbatch_options: ${{ matrix.sbatch_options }}
output_dir: ${{ matrix.output_dir || '' }}
workdir: ${{ matrix.workdir || '' }}
template_data: |
cmake_options:
- -DENABLE_MPI=ON
- -DENABLE_ACC=ON
- -DENABLE_CUDA=ON
- -DSKIP_TEST_atlas_test_field_foreach=TRUE
- ${{ matrix.cmake_options || '' }}
ctest_options: ${{ matrix.ctest_options || '' }}
dependencies:
ecmwf/ecbuild:
version: develop
ecmwf/eckit:
version: develop
cmake_options:
- -DENABLE_MPI=ON
- -DENABLE_CUDA=OFF
- -DENABLE_TESTS=OFF
- -DENABLE_ECKIT_SQL=OFF
- -DENABLE_ECKIT_CMD=OFF
- -DENABLE_AIO=OFF
- -DENABLE_WARNINGS=OFF
- ${{ matrix.cmake_options || '' }}
ecmwf/fckit:
version: develop
cmake_options:
- -DENABLE_TESTS=OFF
- ${{ matrix.cmake_options || '' }}
ecmwf-ifs/fiat:
version: develop
cmake_options:
- -DENABLE_MPI=ON
- -DENABLE_TESTS=OFF
- ${{ matrix.cmake_options || '' }}
ecmwf-ifs/ectrans:
version: develop
cmake_options:
- -DENABLE_MPI=ON
- -DENABLE_ACC=ON
- -DENABLE_GPU=ON
- -DENABLE_TESTS=OFF
- ${{ matrix.cmake_options || '' }}
template: |
set +x
module_load() {
echo "+ module load $1"
module load $1
}
{% for module in "${{ join(matrix.modules, ',') }}".split(',') %}
module_load {{module}}
{% endfor %}
echo "+ module list"
module list
BASEDIR=$PWD
export CMAKE_TEST_LAUNCHER="srun;-n;1"
export CMAKE_PREFIX_PATH=$BASEDIR/install:$CMAKE_PREFIX_PATH
{% for repo_name, options in dependencies.items() %}
name=$(basename {{repo_name}})
echo "::group::Get dependency $name"
echo "+ mkdir -p $name"
mkdir -p $name
echo "+ pushd $name"
pushd $name
echo "+ git init"
git init
echo "+ git remote add origin ${{ github.server_url }}/{{repo_name}}"
git remote add origin ${{ github.server_url }}/{{repo_name}}
echo "+ git fetch origin {{options['version']}}"
git fetch origin {{options['version']}}
echo "+ git reset --hard FETCH_HEAD"
git reset --hard FETCH_HEAD
echo "+ cmake -G Ninja -S . -B build {{ options['cmake_options']|join(' ') }}"
cmake -G Ninja -S . -B build {{ options['cmake_options']|join(' ') }}
start=`date +%s`
echo "+ cmake --build build"
cmake --build build
end=`date +%s`
runtime=$((end-start))
echo "Build $name took $runtime seconds"
echo "+ cmake --install build --prefix \$BASEDIR/install/$name"
cmake --install build --prefix $BASEDIR/install/$name
echo "+ export PATH=\$BASEDIR/install/$name/bin:\$PATH"
export PATH=$BASEDIR/install/$name/bin:$PATH
echo "+ popd"
popd
echo "::endgroup::"
{% endfor %}
REPO=${{ github.event.pull_request.head.repo.full_name || github.repository }}
SHA=${{ github.event.pull_request.head.sha || github.sha }}
name=$(basename $REPO)
echo "::group::Checkout $name"
echo "+ mkdir -p $name"
mkdir -p $name
echo "+ pushd $name"
pushd $name
echo "+ git init"
git init
echo "+ git remote add origin ${{ github.server_url }}/$REPO"
git remote add origin ${{ github.server_url }}/$REPO
echo "+ git fetch origin $SHA"
git fetch origin $SHA
echo "+git reset --hard FETCH_HEAD"
git reset --hard FETCH_HEAD
echo "+ popd"
popd
echo "::endgroup::"
echo "::group::Build $name"
echo "+ cmake -G Ninja -S $name -B build {{ cmake_options|join(' ') }}"
cmake -G Ninja -S $name -B build {{ cmake_options|join(' ') }}
start=`date +%s`
echo "+ cmake --build build"
cmake --build build
end=`date +%s`
runtime=$((end-start))
echo "Build $name took $runtime seconds"
echo "::endgroup::"
echo "::group::Test $name"
export ATLAS_FINALISES_MPI=1
echo "+ ctest --test-dir build --output-on-failure {{ ctest_options }}"
ctest --test-dir build --output-on-failure {{ ctest_options }}
echo "::endgroup::"
echo "::group::Install $name"
echo "+ cmake --install build --prefix $BASEDIR/install/$name"
cmake --install build --prefix $BASEDIR/install/$name
echo "+ export PATH=\$BASEDIR/install/$name/bin:\$PATH"
export PATH=$BASEDIR/install/$name/bin:$PATH
echo "::endgroup::"
echo "::group::Verify $name installation"
echo "+ atlas --info"
atlas --info
echo "::endgroup::"
echo "::group::Cleanup"
set -x
rm -r $name
rm -r build
rm -r $BASEDIR/install
{% for repo_name in dependencies.keys() %}
name=$(basename {{repo_name}})
rm -r $name
{% endfor %}
echo "::endgroup::"
set +x
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