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Add offsets to probe sampler with new unit test (#1277) #150

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Add offsets to probe sampler with new unit test (#1277)

Add offsets to probe sampler with new unit test (#1277) #150

Workflow file for this run

.github/workflows/ci.yml at 3ad9250
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-latest
steps:
- name: Clone
uses: actions/checkout@v4
- name: Check formatting
uses: DoozyX/[email protected]
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-latest, 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-latest
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:" 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 ${{matrix.ctest_args}} --output-on-failure
GPU-Nvidia:
name: GPU-CUDA
needs: Formatting
runs-on: ubuntu-20.04
strategy:
matrix:
cuda_ver: [11.4]
include:
- cuda_ver: "11.4"
cuda_pkg: 11-4
cuda_extra: libcurand-dev-11-4 cuda-cupti-dev-11-4
steps:
- name: Clone
uses: actions/checkout@v4
with:
submodules: true
- name: Setup
run: |
echo "NPROCS=$(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: |
${{github.workspace}}/submods/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" | sudo tee /etc/apt/sources.list.d/cuda.list
sudo apt-get update
sudo apt-get install -y \
cuda-command-line-tools-${{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}} ${{matrix.cuda_extra}}
- name: Configure and build
run: |
export PATH=/usr/local/nvidia/bin:/usr/local/cuda-${{matrix.cuda_ver}}/bin:${PATH}
export LD_LIBRARY_PATH=/usr/local/nvidia/lib:/usr/local/nvidia/lib64:/usr/local/cuda-${{matrix.cuda_ver}}/lib:${LD_LIBRARY_PATH}
cmake -B build-${{matrix.cuda_pkg}} \
-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=70 \
-DCMAKE_CUDA_COMPILER_LAUNCHER:STRING=ccache \
-DCMAKE_CXX_COMPILER_LAUNCHER:STRING=ccache \
${{github.workspace}}
ccache -z
cmake --build build-${{matrix.cuda_pkg}} --parallel ${{env.NPROCS}}
- name: Ccache Report
run: |
ccache -s
ls ~/.cache/ccache
du -hs ~/.cache/ccache
GPU-AMD:
name: GPU-HIP
needs: Formatting
runs-on: ubuntu-20.04
steps:
- name: Clone
uses: actions/checkout@v4
with:
submodules: true
- name: Setup
run: |
echo "NPROCS=$(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: |
${{github.workspace}}/submods/amrex/.github/workflows/dependencies/ubuntu_free_disk_space.sh
wget -q -O - https://repo.radeon.com/rocm/rocm.gpg.key | sudo apt-key add -
echo 'deb [arch=amd64] https://repo.radeon.com/rocm/apt/5.6.1/ ubuntu main' | sudo tee /etc/apt/sources.list.d/rocm.list
echo 'export PATH=/opt/rocm/llvm/bin:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin:$PATH' | sudo tee -a /etc/profile.d/rocm.sh
sudo apt-get update
sudo apt-get install -y \
build-essential rocm-dev rocrand-dev rocprim-dev
- name: Configure and build
run: |
source /etc/profile.d/rocm.sh
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 ${{env.NPROCS}}
- name: Ccache Report
run: |
ccache -s
ls ~/.cache/ccache
du -hs ~/.cache/ccache
GPU-Intel:
name: GPU-SYCL
needs: Formatting
runs-on: ubuntu-20.04
steps:
- name: Clone
uses: actions/checkout@v4
with:
submodules: true
- name: Setup
run: |
echo "NPROCS=$(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 $2}')
Lint-clang-tidy:
needs: Formatting
runs-on: ubuntu-latest
steps:
- name: Clone
uses: actions/checkout@v4
with:
submodules: true
- name: Setup
run: |
echo "NPROCS=$(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_ALL_WARNINGS:BOOL=ON \
-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 | grep "warning:" | 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 $2}')
Lint-codeql:
needs: Formatting
runs-on: ubuntu-latest
steps:
- name: Clone
uses: actions/checkout@v4
with:
submodules: true
- name: Initialize CodeQL
uses: github/codeql-action/init@v3
with:
languages: cpp
queries: +security-and-quality
config-file: ./.github/codeql/codeql-config.yml
- name: Configure
run: |
echo "NPROCS=$(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-latest
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-latest
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 && \
quick-create-dev -s amr-wind+hypre+netcdf@main && \
spack -e e4s-build config add view:true && \
spack -e e4s-build add cmake && \
spack -e e4s-build concretize && \
spack manager external ${EXAWIND_MANAGER}/environments/e4s-build --exclude amr-wind && \
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-latest
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