Consolidate flux register calculation into one place #2246

Workflow file for this run

	name: PeleC-CI

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

	jobs:
	Formatting:
	runs-on: ubuntu-latest
	steps:
	- name: Clone
	uses: actions/checkout@v3
	- name: Check formatting
	uses: DoozyX/[email protected]
	with:
	source: './Source ./Exec'
	exclude: '.'
	extensions: 'H,h,cpp'
	clangFormatVersion: 14
	CPU-GNUmake:
	needs: Formatting
	runs-on: ubuntu-latest
	steps:
	- name: Cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{github.token}}
	- name: Clone
	uses: actions/checkout@v3
	with:
	submodules: true
	- name: Setup
	working-directory: ./Exec/RegTests/PMF
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	#printf "CC=gcc-10\nCXX=g++-10\nFC=gfortran-10\nF90=gfortran-10" \
	# >> ${{github.workspace}}/Submodules/AMReX/Tools/GNUMake/Make.local
	make COMP=gnu USE_MPI=FALSE DEBUG=TRUE TPL
	make COMP=llvm USE_MPI=FALSE DEBUG=TRUE PRECISION=FLOAT TPL
	- name: PMF debug make
	working-directory: ./Exec/RegTests/PMF
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	make -j ${{env.NPROCS}} COMP=gnu USE_MPI=FALSE DEBUG=TRUE 2>&1 \| tee -a build-output.txt
	- name: PMF debug test
	working-directory: ./Exec/RegTests/PMF
	run: ./PeleC3d.gnu.DEBUG.ex pmf-lidryer-arkode.inp max_step=2 amr.plot_files_output=0 amr.checkpoint_files_output=0
	- name: PMF debug report
	working-directory: ./Exec/RegTests/PMF
	run: \|
	egrep "warning:\|error:" build-output.txt \
	\| egrep -v "Submodules/AMReX\|Submodules/sundials\|Submodules/GoogleTest\|GNUmakefile" \
	\| 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}
	- name: EB debug build
	working-directory: ./Exec/RegTests/EB-C10
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	make -j ${{env.NPROCS}} COMP=gnu USE_MPI=FALSE DEBUG=TRUE 2>&1 \| tee -a build-output.txt
	- name: EB debug test
	working-directory: ./Exec/RegTests/EB-C10
	run: ./PeleC3d.gnu.DEBUG.ex eb-c10.inp max_step=2 amr.plot_files_output=0 amr.checkpoint_files_output=0
	- name: EB debug report
	working-directory: ./Exec/RegTests/EB-C10
	run: \|
	egrep "warning:\|error:" build-output.txt \
	\| egrep -v "Submodules/AMReX\|Submodules/sundials\|Submodules/GoogleTest\|GNUmakefile" \
	\| 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}
	- name: TG debug single precision build
	working-directory: ./Exec/RegTests/TG
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	make -j ${{env.NPROCS}} COMP=llvm USE_MPI=FALSE DEBUG=TRUE PRECISION=FLOAT 2>&1 \| tee -a build-output.txt
	- name: TG debug single precision test
	working-directory: ./Exec/RegTests/TG
	run: ./PeleC3d.llvm.FLOAT.DEBUG.ex tg-2.inp max_step=2 amr.plot_files_output=0 amr.checkpoint_files_output=0
	- name: TG debug single precision report
	working-directory: ./Exec/RegTests/TG
	run: \|
	egrep "warning:\|error:" build-output.txt \
	\| egrep -v "Submodules/AMReX\|Submodules/sundials\|Submodules/GoogleTest\|GNUmakefile" \
	\| 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}
	- name: Soot debug build
	working-directory: ./Exec/RegTests/Soot-Flame
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	make -j ${{env.NPROCS}} COMP=gnu USE_MPI=FALSE DEBUG=TRUE 2>&1 \| tee -a build-output.txt
	- name: Soot debug report
	working-directory: ./Exec/RegTests/Soot-Flame
	run: \|
	egrep "warning:\|error:" build-output.txt \
	\| egrep -v "Submodules/AMReX\|Submodules/sundials\|Submodules/GoogleTest\|GNUmakefile\|Submodules/PeleMP" \
	\| egrep -v "Submodules/PelePhysics/Support/Mechanism/Models" \| 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}
	- name: Spray debug build
	working-directory: ./Exec/RegTests/Spray-Conv
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	make -j ${{env.NPROCS}} COMP=gnu USE_MPI=FALSE DEBUG=TRUE 2>&1 \| tee -a build-output.txt
	- name: Spray debug report
	working-directory: ./Exec/RegTests/Spray-Conv
	run: \|
	egrep "warning:\|error:" build-output.txt \
	\| egrep -v "Submodules/AMReX\|Submodules/sundials\|Submodules/GoogleTest\|GNUmakefile\|Submodules/PeleMP" \
	\| egrep -v "Submodules/PelePhysics/Support/Mechanism/Models" \| 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-latest, macos-latest]
	build_type: [Release, Debug]
	include:
	- os: macos-latest
	install_deps: brew install mpich automake ninja
	comp: llvm
	procs: $(sysctl -n hw.ncpu)
	- os: ubuntu-latest
	install_deps: sudo apt-get update && sudo apt-get install mpich libmpich-dev ninja-build
	comp: gnu
	procs: $(nproc)
	- build_type: Release
	ctest_args: -LE no-ci
	- build_type: Debug
	ctest_args: -R eb-c12
	exclude:
	- os: macos-latest
	build_type: Debug
	steps:
	- name: Cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{github.token}}
	- name: Clone
	uses: actions/checkout@v3
	with:
	submodules: true
	- name: Python
	uses: actions/setup-python@v3
	with:
	python-version: '3.8'
	- name: Setup
	run: \|
	echo "NPROCS=${{matrix.procs}}" >> $GITHUB_ENV
	cmake -E make_directory ${{runner.workspace}}/deps
	- name: Dependencies
	run: \|
	# Install MPI
	${{matrix.install_deps}}
	# Install Python packages
	python -m pip install --upgrade pip
	pip install nose numpy pandas
	- name: MASA
	run: \|
	# Install MetaPhysicL
	cd ${{runner.workspace}}/deps
	git clone --recursive https://github.com/roystgnr/MetaPhysicL.git ${{runner.workspace}}/deps/MetaPhysicL
	cd ${{runner.workspace}}/deps/MetaPhysicL
	./bootstrap
	./configure --prefix="${{runner.workspace}}/deps/install/MetaPhysicL"
	make -j ${{env.NPROCS}}
	make install
	# Install MASA
	cd ${{runner.workspace}}/deps
	git clone --recursive https://github.com/manufactured-solutions/MASA.git ${{runner.workspace}}/deps/MASA
	cd ${{runner.workspace}}/deps/MASA
	./bootstrap
	./configure CXX='mpicxx -std=c++11' CC=mpicc \
	METAPHYSICL_DIR="${{runner.workspace}}/deps/install/MetaPhysicL" \
	--prefix="${{runner.workspace}}/deps/install/MASA"
	make -j ${{env.NPROCS}}
	make install
	- name: Configure
	run: \|
	(for DIM in 2 3; do \
	printf "\n-------- Configuring ${DIM}D --------\n"; \
	cmake -G Ninja \
	-B${{runner.workspace}}/build-${DIM}d-${{matrix.os}}-${{matrix.build_type}} \
	-DCMAKE_INSTALL_PREFIX:PATH=${{runner.workspace}}/install-${DIM}d-${{matrix.os}}-${{matrix.build_type}} \
	-DCMAKE_BUILD_TYPE:STRING=${{matrix.build_type}} \
	-DPELEC_DIM:STRING=${DIM} \
	-DPELEC_ENABLE_MPI:BOOL=ON \
	-DPELEC_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELEC_ENABLE_MASA:BOOL=ON \
	-DMASA_ROOT:PATH=${{runner.workspace}}/deps/install/MASA \
	${{github.workspace}}; \
	if [ $? -ne 0 ]; then exit 1; fi \
	done)
	- name: Build
	run: \|
	(for DIM in 2 3; do \
	printf "\n-------- Building ${DIM}D --------\n"; \
	cmake --build ${{runner.workspace}}/build-${DIM}d-${{matrix.os}}-${{matrix.build_type}} \
	--parallel ${{env.NPROCS}} 2>&1 \| tee -a ${{runner.workspace}}/build-output.txt; \
	if [ ${PIPESTATUS[0]} -ne 0 ]; then exit 1; fi \
	done)
	- name: Report
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	egrep "warning:\|error:" ${{runner.workspace}}/build-output.txt \
	\| egrep -v "Submodules/AMReX\|Submodules/sundials\|Submodules/GoogleTest" \
	\| egrep -v "ld: 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}}; \
	ctest -j ${{env.NPROCS}} ${{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-20.04
	strategy:
	matrix:
	cuda_ver: [11.4]
	include:
	- cuda_ver: "11.4"
	cuda_pkg: 11-4
	steps:
	- name: Cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{github.token}}
	- name: Clone
	uses: actions/checkout@v3
	with:
	submodules: true
	- name: Dependencies
	run: \|
	curl -O https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.0-1_all.deb
	sudo dpkg -i cuda-keyring_1.0-1_all.deb
	sudo apt-get update
	sudo apt-get install -y ninja-build \
	cuda-command-line-tools-${{matrix.cuda_pkg}} \
	cuda-compiler-${{matrix.cuda_pkg}} cuda-minimal-build-${{matrix.cuda_pkg}} \
	cuda-nvml-dev-${{matrix.cuda_pkg}} cuda-nvtx-${{matrix.cuda_pkg}} \
	libcurand-dev-${{matrix.cuda_pkg}} cuda-cupti-dev-${{matrix.cuda_pkg}} \
	libcusolver-dev-${{matrix.cuda_pkg}} libcusparse-dev-${{matrix.cuda_pkg}} \
	libcublas-dev-${{matrix.cuda_pkg}}
	- name: Configure
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	export PATH=/usr/local/nvidia/bin:/usr/local/cuda-${{matrix.cuda_ver}}/bin:${PATH}
	export LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda-${{matrix.cuda_ver}}/lib:${LD_LIBRARY_PATH}
	cmake -G "Unix Makefiles" -Bbuild-${{matrix.cuda_pkg}} \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DPELEC_ENABLE_MPI:BOOL=OFF \
	-DPELEC_ENABLE_CUDA:BOOL=ON \
	-DAMReX_CUDA_ERROR_CAPTURE_THIS:BOOL=ON \
	-DCMAKE_CUDA_ARCHITECTURES:STRING=70 \
	${{github.workspace}}
	- name: Build
	run: cmake --build build-${{matrix.cuda_pkg}} --parallel ${{env.NPROCS}}
	GPU-AMD:
	name: GPU-HIP
	needs: [Formatting, CPU-GNUmake]
	runs-on: ubuntu-20.04
	steps:
	- name: Cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{github.token}}
	- name: Clone
	uses: actions/checkout@v3
	with:
	submodules: true
	- name: Dependencies
	run: \|
	curl -O https://repo.radeon.com/rocm/rocm.gpg.key
	sudo apt-key add rocm.gpg.key
	echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/debian/ ubuntu main' \
	\| sudo tee /etc/apt/sources.list.d/rocm.list
	echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \
	\| sudo tee -a /etc/profile.d/rocm.sh
	sudo apt-get update
	sudo apt-get install -y ninja-build rocm-dev roctracer-dev rocprofiler-dev rocrand-dev rocprim-dev rocm-libs
	- name: Configure
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	source /etc/profile.d/rocm.sh
	which clang
	which hipcc
	cmake -G Ninja -B${{runner.workspace}}/build-hip \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DCMAKE_CXX_COMPILER:STRING=$(which hipcc) \
	-DCMAKE_C_COMPILER:STRING=$(which clang) \
	-DCMAKE_CXX_STANDARD:STRING=17 \
	-DPELEC_ENABLE_MPI:BOOL=OFF \
	-DPELEC_ENABLE_HIP:BOOL=ON \
	-DAMReX_AMD_ARCH:STRING=gfx908 \
	-DCMAKE_HIP_ARCHITECTURES:STRING=gfx908 \
	-DAMDGPU_TARGETS:STRING=gfx908 \
	-DGPU_TARGETS:STRING=gfx908 \
	-DPELEC_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELEC_ENABLE_MASA:BOOL=OFF \
	${{github.workspace}}
	- name: Build
	working-directory: ${{runner.workspace}}/build-hip
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	source /etc/profile.d/rocm.sh
	cmake --build . --parallel ${{env.NPROCS}}
	GPU-Intel:
	name: GPU-SYCL
	needs: [Formatting, CPU-GNUmake]
	runs-on: ubuntu-latest
	steps:
	- name: Cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{github.token}}
	- name: Clone
	uses: actions/checkout@v3
	with:
	submodules: true
	#- name: Update GCC
	# uses: egor-tensin/setup-gcc@v1
	# with:
	# version: 11
	# platform: x64
	- name: Dependencies
	run: \|
	sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
	sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
	echo "deb https://apt.repos.intel.com/oneapi all main" \
	\| sudo tee /etc/apt/sources.list.d/oneAPI.list
	sudo apt-get update
	sudo apt-get install -y ninja-build intel-oneapi-compiler-dpcpp-cpp intel-oneapi-mkl-devel
	- name: Configure
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	set +e
	source /opt/intel/oneapi/setvars.sh
	set -e
	cmake -G Ninja -B${{runner.workspace}}/build-sycl \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DCMAKE_CXX_COMPILER:STRING=$(which icpx) \
	-DCMAKE_C_COMPILER:STRING=$(which icx) \
	-DCMAKE_CXX_FLAGS:STRING=-fsycl \
	-DPELEC_ENABLE_MPI:BOOL=OFF \
	-DPELEC_ENABLE_MASA:BOOL=OFF \
	-DPELEC_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELEC_ENABLE_SYCL:BOOL=ON \
	${{github.workspace}}
	- name: Build
	working-directory: ${{runner.workspace}}/build-sycl
	run: \|
	set +e
	source /opt/intel/oneapi/setvars.sh
	set -e
	cmake --build . --parallel ${{env.NPROCS}}
	Lint-cppcheck:
	needs: Formatting
	runs-on: macos-12
	steps:
	- name: Cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{github.token}}
	- name: Clone
	uses: actions/checkout@v3
	with:
	submodules: true
	- name: Dependencies
	run: \|
	brew install cppcheck
	- name: Configure
	run: \|
	cmake -B${{runner.workspace}}/build-cppcheck \
	-DPELEC_ENABLE_MPI:BOOL=OFF \
	-DPELEC_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELEC_ENABLE_MASA:BOOL=OFF \
	-DPELEC_ENABLE_CPPCHECK:BOOL=ON \
	${{github.workspace}}
	- name: Check
	working-directory: ${{runner.workspace}}/build-cppcheck
	run: make cppcheck
	- name: Full report
	working-directory: ${{runner.workspace}}/build-cppcheck/cppcheck
	run: cat cppcheck-full-report.txt
	- name: Short report
	working-directory: ${{runner.workspace}}/build-cppcheck/cppcheck
	run: \|
	echo "::add-matcher::.github/problem-matchers/cppcheck.json"
	awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' < cppcheck-report.txt > cppcheck-warnings.txt
	cat cppcheck-warnings.txt
	export return=$(tail -n 1 cppcheck-warnings.txt \| awk '{print $2}')
	exit ${return}
	Lint-clang-tidy:
	needs: Formatting
	runs-on: ubuntu-latest
	steps:
	- name: Cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{github.token}}
	- name: Clone
	uses: actions/checkout@v3
	with:
	submodules: true
	- name: Dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y ninja-build
	- name: Configure
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	cmake -G Ninja -B${{runner.workspace}}/build-clang-tidy \
	-DCMAKE_BUILD_TYPE:STRING=Debug \
	-DCMAKE_CXX_COMPILER:STRING=clang++ \
	-DCMAKE_C_COMPILER:STRING=clang \
	-DPELEC_ENABLE_MPI:BOOL=OFF \
	-DPELEC_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELEC_ENABLE_MASA:BOOL=OFF \
	-DPELEC_ENABLE_CLANG_TIDY:BOOL=ON \
	${{github.workspace}}
	- name: Check
	working-directory: ${{runner.workspace}}/build-clang-tidy
	run: \|
	cmake --build . --parallel ${{env.NPROCS}} 2>&1 \| tee -a clang-tidy-full-report.txt
	egrep "warning:\|error:" clang-tidy-full-report.txt \
	\| egrep -v "Submodules/AMReX\|Submodules/sundials\|Submodules/GoogleTest" \
	\| egrep -v "ld: warning:" \| sort \| uniq \
	\| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > clang-tidy-warnings.txt
	- 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-latest
	steps:
	- name: Cancel previous runs
	uses: styfle/[email protected]
	with:
	access_token: ${{github.token}}
	- name: Clone
	uses: actions/checkout@v3
	with:
	submodules: true
	- name: Dependencies
	run: \|
	sudo apt-get update
	sudo apt-get install -y ninja-build
	- name: Initialize CodeQL
	uses: github/codeql-action/init@v2
	with:
	languages: cpp
	queries: +security-and-quality
	config-file: ./.github/codeql/codeql-config.yml
	- name: Configure
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	cmake -G Ninja -B${{runner.workspace}}/build-codeql \
	-DCMAKE_BUILD_TYPE:STRING=Debug \
	-DCMAKE_CXX_COMPILER:STRING=clang++ \
	-DCMAKE_C_COMPILER:STRING=clang \
	-DPELEC_ENABLE_MPI:BOOL=OFF \
	-DPELEC_ENABLE_FCOMPARE_FOR_TESTS:BOOL=OFF \
	-DPELEC_ENABLE_MASA:BOOL=OFF \
	-DPELEC_ENABLE_CLANG_TIDY:BOOL=OFF \
	${{github.workspace}}
	- name: Build
	working-directory: ${{runner.workspace}}/build-codeql
	run: \|
	cmake --build . --parallel ${{env.NPROCS}}
	- name: Perform CodeQL Analysis
	uses: github/codeql-action/analyze@v2
	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@v2
	with:
	sarif_file: sarif-results/cpp.sarif

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Consolidate flux register calculation into one place #2246

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Consolidate flux register calculation into one place #2246

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