Specified Monin-Obukhov Length #5792

Workflow file for this run

	name: AMR-Wind-CI

	on:
	push:
	branches: [main]
	pull_request:
	branches: [main]

	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/clang-format-lint-action@v0.18.2
	with:
	source: './amr-wind ./unit_tests ./tools/utilities'
	exclude: '.'
	extensions: 'H,h,cpp'
	clangFormatVersion: 18
	CPU:
	needs: Formatting
	runs-on: ${{matrix.os}}
	strategy:
	matrix:
	os: [ubuntu-22.04, macos-latest]
	build_type: [Release, Debug]
	openmp_flag: [OpenMP, NoOpenMP]
	include:
	- os: macos-latest
	install_deps: brew install mpich ccache
	comp: llvm
	procs: $(sysctl -n hw.ncpu)
	ccache_cache: /Users/runner/Library/Caches/ccache
	- os: ubuntu-22.04
	install_deps: sudo apt-get install -y mpich libmpich-dev
	comp: gnu
	procs: $(nproc)
	ccache_cache: ~/.cache/ccache
	- build_type: Release
	ctest_args: -LE no_ci
	ccache_size: 150M
	- build_type: Debug
	ctest_args: -L unit
	ccache_size: 500M
	exclude:
	- os: macos-latest
	build_type: Debug
	- os: macos-latest
	openmp_flag: OpenMP
	- build_type: Release
	openmp_flag: OpenMP
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: true
	- name: Dependencies
	run: ${{matrix.install_deps}}
	- name: Setup
	run: \|
	echo "NPROCS=${{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}}" >> $GITHUB_ENV
	- name: Install Ccache
	run: \|
	if [ "${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.openmp_flag}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-${{matrix.os}}-${{matrix.build_type}}-${{matrix.openmp_flag}}-git-
	- name: Configure
	run: \|
	cmake -B ${{runner.workspace}}/build-ci-${{matrix.build_type}}-${{matrix.openmp_flag}} \
	-DCMAKE_INSTALL_PREFIX:PATH=${{runner.workspace}}/install-${{matrix.build_type}}-${{matrix.openmp_flag}} \
	-DCMAKE_BUILD_TYPE:STRING=${{matrix.build_type}} \
	-DAMR_WIND_ENABLE_MPI:BOOL=ON \
	-DAMR_WIND_ENABLE_OPENMP:BOOL=${{ matrix.openmp_flag == 'OpenMP' && 'ON' \|\| 'OFF' }} \
	-DAMR_WIND_ENABLE_TESTS:BOOL=ON \
	-DAMR_WIND_TEST_WITH_FCOMPARE:BOOL=OFF \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}
	- name: Build
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	ccache -z
	set -eu -o pipefail
	cmake --build ${{runner.workspace}}/build-ci-${{matrix.build_type}}-${{matrix.openmp_flag}} --parallel ${{env.NPROCS}} 2>&1 \| \
	tee -a ${{runner.workspace}}/build-ci-${{matrix.build_type}}-${{matrix.openmp_flag}}/build-output.txt
	- name: Ccache Report
	run: \|
	ccache -s
	ls ${{matrix.ccache_cache}}
	du -hs ${{matrix.ccache_cache}}
	- name: Report
	working-directory: ${{runner.workspace}}/build-ci-${{matrix.build_type}}-${{matrix.openmp_flag}}
	run: \|
	echo "::add-matcher::.github/problem-matchers/gcc.json"
	egrep "Warning:\|Error:\|warning:\|error:" build-output.txt \| egrep -v "submods" \
	\| egrep -v "ld: warning:" \| egrep -v "lto-wrapper: warning:" \| sort \| uniq \
	\| awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > build-output-warnings.txt
	cat build-output-warnings.txt
	exit $(tail -n 1 build-output-warnings.txt \| awk '{print $2}')
	- name: Test
	working-directory: ${{runner.workspace}}/build-ci-${{matrix.build_type}}-${{matrix.openmp_flag}}
	run: \|
	ctest ${{matrix.ctest_args}} --output-on-failure
	GPU-Nvidia:
	name: GPU-CUDA
	needs: Formatting
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: true
	- name: Setup
	run: \|
	echo "NPROCS=$(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=200M" >> $GITHUB_ENV
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache/ccache
	key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-git-
	- name: Prepare CUDA environment
	run: \|
	${{github.workspace}}/submods/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
	wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2404/x86_64/cuda-keyring_1.1-1_all.deb
	sudo dpkg -i cuda-keyring_1.1-1_all.deb
	sudo apt-get update
	sudo apt-get install -y cuda-command-line-tools-12-6 cuda-compiler-12-6 cuda-minimal-build-12-6 cuda-nvml-dev-12-6 cuda-nvtx-12-6 libcurand-dev-12-6 cuda-cupti-dev-12-6 libcusparse-dev-12-6
	- name: Configure and build
	run: \|
	export PATH=/usr/local/nvidia/bin:/usr/local/cuda-12.6/bin:${PATH}
	export LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda-12.6/lib:${LD_LIBRARY_PATH}
	cmake -B build-cuda \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DAMR_WIND_ENABLE_MPI:BOOL=OFF \
	-DAMR_WIND_ENABLE_CUDA:BOOL=ON \
	-DAMReX_CUDA_ERROR_CAPTURE_THIS:BOOL=ON \
	-DCMAKE_CUDA_COMPILE_SEPARABLE_COMPILATION:BOOL=ON \
	-DCMAKE_CUDA_ARCHITECTURES=80 \
	-DCMAKE_CUDA_COMPILER_LAUNCHER:STRING=ccache \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}
	ccache -z
	cmake --build build-cuda --parallel ${{env.NPROCS}}
	- name: Ccache Report
	run: \|
	ccache -s
	ls ~/.cache/ccache
	du -hs ~/.cache/ccache
	GPU-AMD:
	name: GPU-HIP
	needs: Formatting
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: true
	- name: Setup
	run: \|
	echo "NPROCS=$(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=50M" >> $GITHUB_ENV
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache/ccache
	key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-git-
	- name: Prepare HIP environment
	run: \|
	${{github.workspace}}/submods/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
	sudo mkdir --parents --mode=0755 /etc/apt/keyrings
	wget https://repo.radeon.com/rocm/rocm.gpg.key -O - \| gpg --dearmor \| sudo tee /etc/apt/keyrings/rocm.gpg > /dev/null
	echo "deb [arch=amd64 signed-by=/etc/apt/keyrings/rocm.gpg] https://repo.radeon.com/rocm/apt/6.2.1 noble main" \| sudo tee --append /etc/apt/sources.list.d/rocm.list
	echo -e 'Package: *\nPin: release o=repo.radeon.com\nPin-Priority: 600' \| sudo tee /etc/apt/preferences.d/rocm-pin-600
	echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' \| sudo tee -a /etc/profile.d/rocm.sh
	sudo apt-get update
	sudo apt-get install -y --no-install-recommends build-essential rocm-dev rocrand-dev rocprim-dev hiprand-dev rocsparse-dev
	- name: Configure and build
	run: \|
	source /etc/profile.d/rocm.sh
	hipcc --version
	hipconfig --full
	which clang
	which clang++
	cmake -B build \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DAMR_WIND_ENABLE_MPI:BOOL=OFF \
	-DAMR_WIND_ENABLE_ROCM:BOOL=ON \
	-DCMAKE_CXX_COMPILER:STRING=$(which clang++) \
	-DCMAKE_C_COMPILER:STRING=$(which clang) \
	-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
	-DAMReX_AMD_ARCH:STRING=gfx90a \
	-DCMAKE_HIP_ARCHITECTURES:STRING=gfx90a \
	-DAMDGPU_TARGETS:STRING=gfx90a \
	-DGPU_TARGETS:STRING=gfx90a \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}
	ccache -z
	cmake --build build --parallel ${{env.NPROCS}}
	- name: Ccache Report
	run: \|
	ccache -s
	ls ~/.cache/ccache
	du -hs ~/.cache/ccache
	GPU-Intel:
	name: GPU-SYCL
	needs: Formatting
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: true
	- name: Setup
	run: \|
	echo "NPROCS=$(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=50M" >> $GITHUB_ENV
	echo "CCACHE_DEPEND=1" >> $GITHUB_ENV
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache/ccache
	key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-git-
	- name: Prepare SyCL environment
	run: \|
	export DEBIAN_FRONTEND=noninteractive
	${{github.workspace}}/submods/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
	sudo wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
	sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
	echo "deb https://apt.repos.intel.com/oneapi all main" \| sudo tee /etc/apt/sources.list.d/oneAPI.list
	sudo apt-get update
	sudo apt-get install -y intel-oneapi-compiler-dpcpp-cpp intel-oneapi-mkl-devel
	- name: Configure and build
	run: \|
	set +e
	source /opt/intel/oneapi/setvars.sh
	set -e
	cmake -B build-SYCL \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DCMAKE_CXX_COMPILER:STRING=$(which icpx) \
	-DCMAKE_C_COMPILER:STRING=$(which icx) \
	-DAMR_WIND_ENABLE_MPI:BOOL=OFF \
	-DAMR_WIND_ENABLE_SYCL:BOOL=ON \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{github.workspace}}
	ccache -z
	cmake --build build-SYCL --parallel ${{env.NPROCS}}
	- name: Ccache Report
	run: \|
	ccache -s
	ls ~/.cache/ccache
	du -hs ~/.cache/ccache
	# Lint-cppcheck:
	# needs: Formatting
	# runs-on: macos-latest
	# steps:
	# - name: Clone
	# uses: actions/checkout@v4
	# with:
	# submodules: true
	# - name: Dependencies
	# run: brew install cppcheck
	# - name: Configure
	# run: \|
	# echo "NPROCS=$(sysctl -n hw.ncpu)" >> $GITHUB_ENV
	# cmake \
	# -B ${{runner.workspace}}/build-cppcheck \
	# -DAMR_WIND_ENABLE_MPI:BOOL=OFF \
	# -DAMR_WIND_ENABLE_TESTS:BOOL=ON \
	# -DAMR_WIND_TEST_WITH_FCOMPARE:BOOL=OFF \
	# -DAMR_WIND_ENABLE_MASA:BOOL=OFF \
	# -DAMR_WIND_ENABLE_CPPCHECK:BOOL=ON \
	# ${{github.workspace}}
	# - name: Check
	# working-directory: ${{runner.workspace}}/build-cppcheck
	# run: make cppcheck-ci
	# - name: Full report
	# working-directory: ${{runner.workspace}}/build-cppcheck
	# run: cat cppcheck/cppcheck-full-report.txt
	# - name: Short report
	# working-directory: ${{runner.workspace}}/build-cppcheck
	# run: \|
	# echo "::add-matcher::.github/problem-matchers/cppcheck.json"
	# cat cppcheck-ci-report.txt
	# exit $(tail -n 1 cppcheck-ci-report.txt \| awk '{print $2}')
	Lint-clang-tidy:
	needs: Formatting
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: true
	- name: Setup
	run: \|
	echo "NPROCS=$(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" >> $GITHUB_ENV
	- name: Install Ccache
	run: \|
	wget https://github.com/ccache/ccache/releases/download/v4.8/ccache-4.8-linux-x86_64.tar.xz
	sudo curl https://raw.githubusercontent.com/matus-chochlik/ctcache/7fd516e91c17779cbc6fc18bd119313d9532dd90/clang-tidy-cache -Lo /usr/bin/clang-tidy-cache
	tar xvf ccache-4.8-linux-x86_64.tar.xz
	sudo cp -f ccache-4.8-linux-x86_64/ccache /usr/local/bin/
	sudo chmod +x /usr/bin/clang-tidy-cache
	mkdir -p ~/.cache/ctcache
	- name: Set Up Ccache
	uses: actions/cache@v4
	with:
	path: ~/.cache
	key: ccache-${{github.workflow}}-${{github.job}}-git-${{github.sha}}
	restore-keys: \|
	ccache-${{github.workflow}}-${{github.job}}-git-
	- name: Configure
	run: \|
	cmake \
	-B ${{runner.workspace}}/build-clang-tidy \
	-DCMAKE_BUILD_TYPE:STRING=Release \
	-DCMAKE_CXX_COMPILER:STRING=clang++ \
	-DCMAKE_C_COMPILER:STRING=clang \
	-DAMR_WIND_ENABLE_MPI:BOOL=OFF \
	-DAMR_WIND_ENABLE_TESTS:BOOL=ON \
	-DAMR_WIND_TEST_WITH_FCOMPARE:BOOL=OFF \
	-DAMR_WIND_ENABLE_MASA:BOOL=OFF \
	-DAMR_WIND_ENABLE_CLANG_TIDY:BOOL=ON \
	-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
	${{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
	cat clang-tidy-full-report.txt \| egrep "Warning:\|Error:\|warning:\|error:" \| grep -v "submods" \| sort \| uniq \| \
	awk 'BEGIN{i=0}{print $0}{i++}END{print "Warnings: "i}' > clang-tidy-ci-report.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-ci-report.txt
	exit $(tail -n 1 clang-tidy-ci-report.txt \| awk '{print $2}')
	Lint-codeql:
	needs: Formatting
	runs-on: ubuntu-24.04
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: true
	- name: Initialize CodeQL
	uses: github/codeql-action/init@v3
	with:
	languages: cpp
	queries: +security-and-quality
	config-file: ./.github/codeql/codeql-config.yml
	- name: Configure
	run: \|
	echo "NPROCS=$(nproc)" >> $GITHUB_ENV
	cmake \
	-B ${{runner.workspace}}/build-ci-codeql \
	-DCMAKE_INSTALL_PREFIX:PATH=${{runner.workspace}}/install-codeql \
	-DCMAKE_BUILD_TYPE:STRING=Debug \
	-DCMAKE_CXX_COMPILER:STRING=clang++ \
	-DCMAKE_C_COMPILER:STRING=clang \
	-DAMR_WIND_ENABLE_MPI:BOOL=OFF \
	-DAMR_WIND_ENABLE_TESTS:BOOL=ON \
	-DAMR_WIND_TEST_WITH_FCOMPARE:BOOL=OFF \
	-DAMR_WIND_ENABLE_MASA:BOOL=OFF \
	${{github.workspace}}
	- name: Build
	run: \|
	cmake --build ${{runner.workspace}}/build-ci-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: \|
	-/submods/
	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
	Docker:
	needs: Formatting
	runs-on: ubuntu-24.04
	container:
	image: ecpe4s/exawind-snapshot
	env:
	EXAWIND_MANAGER: /exawind-manager
	E4S_MACHINE: true
	steps:
	- name: Clone
	uses: actions/checkout@v4
	with:
	submodules: true
	- name: Test
	run: \|
	/bin/bash -c " \
	source ${EXAWIND_MANAGER}/start.sh && \
	spack-start && \
	mkdir -p ${EXAWIND_MANAGER}/environments/exawind && \
	cd ${EXAWIND_MANAGER}/environments/exawind && \
	ln -s ${GITHUB_WORKSPACE} amr-wind && \
	spack -e e4s-build config add view:true && \
	spack -e e4s-build add cmake^zlib-ng~new_strategies && \
	spack -e e4s-build concretize -f && \
	quick-create-dev -s amr-wind+hypre+netcdf@main && \
	spack manager external ${EXAWIND_MANAGER}/environments/e4s-build --exclude amr-wind && \
	spack concretize -f && \
	spack install && \
	spack cd -b amr-wind && \
	spack build-env amr-wind ctest -j $(nproc) -L unit --output-on-failure \
	"
	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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Specified Monin-Obukhov Length #5792

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Specified Monin-Obukhov Length #5792

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