Composition verification for external sources (#443) #707

Workflow file for this run

	name: PeleLMeX-CI

	on:
	workflow_dispatch:
	push:
	branches: [development]
	pull_request:
	branches: [development]

	concurrency:
	group: ${{github.ref}}-${{github.head_ref}}-ci
	cancel-in-progress: true

	jobs:
	Formatting:
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	- name: Check formatting
	uses: DoozyX/[email protected]
	with:
	source: './Source ./Exec'
	exclude: '.'
	extensions: 'H,h,cpp'
	clangFormatVersion: 18
	CPU-GNUmake:
	needs: Formatting
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Setup
	working-directory: ./Exec/RegTests/FlameSheet
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
	echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
	echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
	echo "CCACHE_MAXSIZE=200M" >> $GITHUB_ENV
	make COMP=gnu USE_MPI=FALSE DEBUG=TRUE TPL
	make COMP=llvm USE_MPI=FALSE DEBUG=TRUE PRECISION=FLOAT TPL
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache/ccache
	key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-git-
	- name: FlameSheet debug make
	working-directory: ./Exec/RegTests/FlameSheet
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	set -eu -o pipefail
	ccache -z
	make -j ${{env.NPROCS}} DIM=2 KEEP_BUILDINFO_CPP=TRUE USE_CCACHE=TRUE COMP=gnu USE_MPI=FALSE DEBUG=TRUE 2>&1 \| tee -a build-output.txt
	- name: FlameSheet ccache report
	working-directory: ./Exec/RegTests/FlameSheet
	run: \|
	ccache -s
	du -hs ~/.cache/ccache
	- name: FlameSheet debug test
	working-directory: ./Exec/RegTests/FlameSheet
	run: ./PeleLMeX2d.gnu.DEBUG.ex flamesheet-drm19-2d.inp amr.max_step=1 amr.plot_int=-1 amr.check_int=-1
	- name: FlameSheet debug report
	working-directory: ./Exec/RegTests/FlameSheet
	run: \|
	egrep "Warning:\|Error:\|warning:\|error:" build-output.txt \
	\| egrep -v "Submodules/amrex\|Submodules/sundials\|Submodules/AMReX-Hydro\|GNUmakefile\|ThirdParty" \
	\| egrep -v "ld: warning:" \| sort \| uniq \
	\| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > warnings.txt
	cat warnings.txt
	export return=$(tail -n 1 warnings.txt \| awk '{print $2}')
	exit ${return}
	CPU-CMake:
	needs: Formatting
	runs-on: ${{matrix.os}}
	strategy:
	matrix:
	os: [ubuntu-22.04, macos-latest]
	build_type: [Release, Debug]
	enable_eb: [EB-OFF, EB-ON]
	include:
	- os: macos-latest
	install_deps: brew install mpich automake ccache
	comp: llvm
	procs: $(sysctl -n hw.ncpu)
	ccache_cache: /Users/runner/Library/Caches/ccache
	- os: ubuntu-22.04
	install_deps: sudo apt-get update && sudo apt-get install mpich libmpich-dev
	comp: gnu
	procs: $(nproc)
	ccache_cache: ~/.cache/ccache
	- build_type: Release
	ctest_args: -LE no-ci
	ccache_size: 100M
	- build_type: Debug
	ctest_args: -R covo
	ccache_size: 500M
	- enable_eb: EB-OFF
	use_eb: "OFF"
	- enable_eb: EB-ON
	use_eb: "ON"
	exclude:
	- os: macos-latest
	build_type: Debug
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.12'
	- name: Setup
	run: \|
	echo "NPROCS=${{matrix.procs}}" >> $GITHUB_ENV
	echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
	echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
	echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
	echo "CCACHE_MAXSIZE=${{matrix.ccache_size}}" >> $GITHUB_ENV
	cmake -E make_directory ${{runner.workspace}}/deps
	if [ "${RUNNER_OS}" != "macOS" ]; then
	${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
	fi
	- name: Dependencies
	run: \|
	# Install MPI
	${{matrix.install_deps}}
	# Install Python packages
	python -m pip install --upgrade pip
	pip install pynose numpy pandas
	- name: Install Ccache
	run: \|
	if [ "${RUNNER_OS}" != "macOS" ]; then
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	fi
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ${{matrix.ccache_cache}}
	key: ccache-${{github.workflow}}-${{github.job}}-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}}-git-
	- name: Configure
	run: \|
	(for DIM in 2 3; do \
	printf "\n-------- Configuring ${DIM}D --------\n"; \
	cmake -B${{runner.workspace}}/build-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}} \
	-DCMAKE_INSTALL_PREFIX:PATH=${{runner.workspace}}/install-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}} \
	-DCMAKE_BUILD_TYPE:STRING=${{matrix.build_type}} \
	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
	-DPELE_DIM:STRING=${DIM} \
	-DPELE_ENABLE_MPI:BOOL=ON \
	-DPELE_ENABLE_EB:BOOL=${{matrix.use_eb}} \
	-DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}; \
	if [ $? -ne 0 ]; then exit 1; fi \
	done)
	- name: Build
	run: \|
	ccache -z
	(for DIM in 2 3; do \
	printf "\n-------- Building ${DIM}D --------\n"; \
	cmake --build ${{runner.workspace}}/build-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}} \
	--parallel ${{env.NPROCS}} 2>&1 \| tee -a ${{runner.workspace}}/build-output.txt; \
	if [ ${PIPESTATUS[0]} -ne 0 ]; then exit 1; fi \
	done)
	- name: Ccache Report
	run: \|
	ccache -s
	du -hs ${{matrix.ccache_cache}}
	- name: Report
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	egrep "Warning:\|Error:\|warning:\|error:" ${{runner.workspace}}/build-output.txt \
	\| egrep -v "Submodules/amrex\|Submodules/sundials\|Submodules/AMReX-Hydro" \
	\| egrep -v "ld: warning:" \| egrep -v "lto-wrapper: warning:" \| sort \| uniq \
	\| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > ${{runner.workspace}}/build-output-warnings.txt
	cat ${{runner.workspace}}/build-output-warnings.txt
	export return=$(tail -n 1 ${{runner.workspace}}/build-output-warnings.txt \| awk '{print $2}')
	exit ${return}
	- name: Test
	run: \|
	(for DIM in 2 3; do \
	printf "\n-------- Testing ${DIM}D --------\n"; \
	cd ${{runner.workspace}}/build-${DIM}d-${{matrix.os}}-${{matrix.build_type}}-${{matrix.enable_eb}}; \
	ctest ${{matrix.ctest_args}} --output-on-failure; \
	if [ $? -ne 0 ]; then exit 1; fi \
	done)
	GPU-Nvidia:
	name: GPU-CUDA
	needs: [Formatting, CPU-GNUmake]
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Setup
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
	echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
	echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
	echo "CCACHE_MAXSIZE=300M" >> $GITHUB_ENV
	- name: Dependencies
	run: \|
	${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
	wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/cuda-keyring_1.1-1_all.deb
	sudo dpkg -i cuda-keyring_1.1-1_all.deb
	sudo apt-get update
	sudo apt-get install -y cuda-command-line-tools-12-6 \
	cuda-compiler-12-6 cuda-minimal-build-12-6 \
	cuda-nvml-dev-12-6 cuda-nvtx-12-6 \
	libcurand-dev-12-6 cuda-cupti-dev-12-6 \
	libcusolver-dev-12-6 libcusparse-dev-12-6 \
	libcublas-dev-12-6 libcurand-dev-12-6 libnvjitlink-12-6
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache/ccache
	key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-git-
	- name: Configure
	run: \|
	export PATH=/usr/local/nvidia/bin:/usr/local/cuda-12.6/bin:${PATH}
	export LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda-12.6/lib:${LD_LIBRARY_PATH}
	cmake -Bbuild-cuda \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
	-DPELE_ENABLE_MPI:BOOL=OFF \
	-DPELE_ENABLE_CUDA:BOOL=ON \
	-DAMReX_CUDA_ERROR_CAPTURE_THIS:BOOL=ON \
	-DCMAKE_CUDA_ARCHITECTURES:STRING=80 \
	-DCMAKE_CUDA_COMPILER_LAUNCHER:STRING=ccache \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}
	- name: Build
	run: \|
	ccache -z
	cmake --build build-cuda --parallel ${{env.NPROCS}}
	- name: Ccache Report
	run: \|
	ccache -s
	du -hs ~/.cache/ccache
	GPU-AMD:
	name: GPU-HIP
	needs: [Formatting, CPU-GNUmake]
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Setup
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
	echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
	echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
	echo "CCACHE_MAXSIZE=80M" >> $GITHUB_ENV
	- name: Dependencies
	run: \|
	${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
	sudo mkdir --parents --mode=0755 /etc/apt/keyrings
	wget https://repo.radeon.com/rocm/rocm.gpg.key -O - \| gpg --dearmor \| sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null
	echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/rocm/apt/6.2.1 noble main" \| sudo tee --append /etc/apt/sources.list.d/rocm.list
	echo -e 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' \| sudo tee /etc/apt/preferences.d/rocm-pin-600
	echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \| sudo tee -a /etc/profile.d/rocm.sh
	sudo apt-get update
	sudo apt-get install -y rocm-dev rocrand-dev rocprim-dev hiprand-dev
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache/ccache
	key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-git-
	- name: Configure
	run: \|
	source /etc/profile.d/rocm.sh
	which clang
	which clang++
	which hipcc
	hipcc --version
	hipconfig --full
	cmake -B${{runner.workspace}}/build-hip \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
	-DCMAKE_CXX_COMPILER:STRING=$(which clang++) \
	-DCMAKE_C_COMPILER:STRING=$(which clang) \
	-DPELE_ENABLE_MPI:BOOL=OFF \
	-DPELE_ENABLE_HIP:BOOL=ON \
	-DAMReX_AMD_ARCH:STRING=gfx90a \
	-DCMAKE_HIP_ARCHITECTURES:STRING=gfx90a \
	-DAMDGPU_TARGETS:STRING=gfx90a \
	-DGPU_TARGETS:STRING=gfx90a \
	-DAMReX_GPU_RDC:BOOL=OFF \
	-DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}
	- name: Build
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	source /etc/profile.d/rocm.sh
	ccache -z
	cmake --build ${{runner.workspace}}/build-hip --parallel ${{env.NPROCS}}
	- name: Ccache Report
	run: \|
	ccache -s
	du -hs ~/.cache/ccache
	GPU-Intel:
	name: GPU-SYCL
	needs: [Formatting, CPU-GNUmake]
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Setup
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
	echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
	echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
	echo "CCACHE_MAXSIZE=80M" >> $GITHUB_ENV
	echo "CCACHE_DEPEND=1" >> $GITHUB_ENV
	- name: Dependencies
	run: \|
	${{github.workspace}}/Submodules/PelePhysics/Submodules/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
	sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
	sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
	echo "deb https://apt.repos.intel.com/oneapi all main" \| sudo tee /etc/apt/sources.list.d/oneAPI.list
	sudo apt-get update
	sudo apt-get install -y intel-oneapi-compiler-dpcpp-cpp=2024.2.1-1079 intel-oneapi-mkl-devel=2024.2.2-15
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache/ccache
	key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-git-
	- name: Configure
	run: \|
	set +e
	source /opt/intel/oneapi/setvars.sh
	set -e
	cmake -B${{runner.workspace}}/build-sycl \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
	-DCMAKE_CXX_COMPILER:STRING=$(which icpx) \
	-DCMAKE_C_COMPILER:STRING=$(which icx) \
	-DCMAKE_CXX_FLAGS:STRING=-fsycl \
	-DPELE_ENABLE_MPI:BOOL=OFF \
	-DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELE_ENABLE_SYCL:BOOL=ON \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}
	- name: Build
	run: \|
	set +e
	source /opt/intel/oneapi/setvars.sh
	set -e
	ccache -z
	cmake --build ${{runner.workspace}}/build-sycl --parallel ${{env.NPROCS}}
	- name: Ccache Report
	run: \|
	ccache -s
	du -hs ~/.cache/ccache
	Lint-clang-tidy:
	needs: Formatting
	runs-on: ubuntu-24.04
	strategy:
	matrix:
	enable_eb: [EB-OFF, EB-ON]
	include:
	- enable_eb: EB-OFF
	use_eb: "OFF"
	- enable_eb: EB-ON
	use_eb: "ON"
	fail-fast: false
	steps:
	- name: Setup
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	echo "CCACHE_COMPRESS=1" >> $GITHUB_ENV
	echo "CCACHE_COMPRESSLEVEL=1" >> $GITHUB_ENV
	echo "CCACHE_LOGFILE=${{github.workspace}}/ccache.log.txt" >> $GITHUB_ENV
	echo "CCACHE_EXTRAFILES=${{github.workspace}}/.clang-tidy" >> $GITHUB_ENV
	echo "CCACHE_MAXSIZE=50M" >> $GITHUB_ENV
	echo "CTCACHE_DIR=~/.cache/ctcache" >> $GITHUB_ENV
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	sudo curl https://raw.githubusercontent.com/matus-chochlik/ctcache/7fd516e91c17779cbc6fc18bd119313d9532dd90/clang-tidy-cache -Lo /usr/bin/clang-tidy-cache
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	sudo chmod +x /usr/bin/clang-tidy-cache
	mkdir -p ~/.cache/ctcache
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache
	key: ccache-${{github.workflow}}-${{github.job}}-${{matrix.enable_eb}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-${{matrix.enable_eb}}-git-
	- name: Configure
	run: \|
	cmake -B${{runner.workspace}}/build-clang-tidy \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
	-DCMAKE_CXX_COMPILER:STRING=clang++ \
	-DCMAKE_C_COMPILER:STRING=clang \
	-DPELE_ENABLE_EB:BOOL=${{matrix.use_eb}} \
	-DPELE_ENABLE_MPI:BOOL=OFF \
	-DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELE_ENABLE_CLANG_TIDY:BOOL=ON \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}
	- name: Check
	working-directory: ${{runner.workspace}}/build-clang-tidy
	run: \|
	#set -eu -o pipefail
	cmake --build . --parallel ${{env.NPROCS}} 2>&1 \| tee -a clang-tidy-full-report.txt
	egrep "Warning:\|Error:\|warning:\|error:" clang-tidy-full-report.txt \
	\| egrep -v "Submodules/amrex\|Submodules/sundials\|Submodules/AMReX-Hydro" \
	\| egrep -v "ld: warning:" \| sort \| uniq \
	\| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > clang-tidy-warnings.txt
	- name: Ccache Report
	run: \|
	ls ~/.cache
	ls ~/.cache/ccache
	du -hs ~/.cache/ccache
	ls ~/.cache/ctcache
	du -hs ~/.cache/ctcache
	ccache -s
	- name: Full report
	working-directory: ${{runner.workspace}}/build-clang-tidy
	run: cat clang-tidy-full-report.txt
	- name: Short report
	working-directory: ${{runner.workspace}}/build-clang-tidy
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	cat clang-tidy-warnings.txt
	export return=$(tail -n 1 clang-tidy-warnings.txt \| awk '{print $2}')
	exit ${return}
	Lint-codeql:
	needs: Formatting
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: recursive
	- name: Initialize CodeQL
	uses: github/codeql-action/init@v3
	with:
	languages: cpp
	queries: +security-and-quality
	config-file: ./.github/codeql/codeql-config.yml
	- name: Configure
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	cmake -B${{runner.workspace}}/build-codeql \
	-DCMAKE_BUILD_TYPE:STRING=Debug \
	-DCMAKE_CXX_COMPILER:STRING=clang++ \
	-DCMAKE_C_COMPILER:STRING=clang \
	-DPELE_ENABLE_MPI:BOOL=OFF \
	-DPELE_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELE_ENABLE_CLANG_TIDY:BOOL=OFF \
	${{github.workspace}}
	- name: Build
	run: \|
	cmake --build ${{runner.workspace}}/build-codeql --parallel ${{env.NPROCS}}
	- name: Perform CodeQL Analysis
	uses: github/codeql-action/analyze@v3
	with:
	category: "/language:cpp"
	upload: False
	output: sarif-results
	- name: Filter CodeQL sarif
	uses: advanced-security/filter-sarif@v1
	with:
	patterns: \|
	-/Submodules/sundials/
	-/Submodules/amrex/
	-/Submodules/AMReX-Hydro/
	input: sarif-results/cpp.sarif
	output: sarif-results/cpp.sarif
	- name: Upload CodeQL sarif
	uses: github/codeql-action/upload-sarif@v3
	with:
	sarif_file: sarif-results/cpp.sarif
	Lint-codespell:
	needs: Formatting
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: false
	- name: Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.10'
	- name: Dependencies
	run: \|
	# Install Python packages
	python -m pip install --upgrade pip
	pip install codespell
	- name: Run codespell
	run: codespell
	Save-PR-Number:
	if: github.event_name == 'pull_request'
	runs-on: ubuntu-24.04
	steps:
	- name: Save PR number
	env:
	PR_NUMBER: ${{ github.event.number }}
	run: \|
	echo $PR_NUMBER > pr_number.txt
	- uses: actions/upload-artifact@v4
	with:
	name: pr_number
	path: pr_number.txt
	retention-days: 1

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Composition verification for external sources (#443) #707

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Composition verification for external sources (#443) #707

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