More openMP: find_min/max() and sum() #1157
Workflow file for this run
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name: Build and ctest and recon_test_pack CI | |
on: | |
push: | |
branches: | |
- master | |
- tof_sino_UCL | |
paths-ignore: | |
- '.appveyor.yml' | |
- 'CITATION.cff' | |
- '**/*.md' | |
- '**/*.html' | |
- '**/*.htm' | |
- '**/*.tex' | |
pull_request: | |
branches: | |
- master | |
- tof_sino_UCL | |
paths-ignore: | |
- '.appveyor.yml' | |
- 'CITATION.cff' | |
- '**/*.md' | |
- '**/*.html' | |
- '**/*.htm' | |
- '**/*.tex' | |
workflow_dispatch: | |
inputs: | |
debug_enabled: | |
description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)' | |
required: false | |
default: false | |
jobs: | |
build: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
matrix: | |
include: | |
- os: ubuntu-latest | |
compiler: gcc | |
compiler_version: 9 | |
cuda_version: "0" | |
BUILD_FLAGS: "-DSTIR_OPENMP=ON" | |
BUILD_TYPE: "Release" | |
parallelproj: "ON" | |
ROOT: "ON" | |
ITK: "OFF" | |
- os: ubuntu-latest | |
compiler: clang | |
#compiler_version: | |
cuda_version: "0" | |
BUILD_FLAGS: "-DSTIR_OPENMP=ON" | |
BUILD_TYPE: "Release" | |
parallelproj: "ON" | |
ROOT: "OFF" | |
# currently using ITK 5.2 which doesn't like clang 14 | |
ITK: "OFF" | |
- os: ubuntu-latest | |
compiler: gcc | |
compiler_version: 10 | |
cuda_version: "0" | |
BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17" | |
BUILD_TYPE: "Debug" | |
parallelproj: "OFF" | |
ROOT: "OFF" | |
ITK: "ON" | |
- os: ubuntu-latest | |
compiler: gcc | |
compiler_version: 12 | |
cuda_version: "0" | |
BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=20" | |
BUILD_TYPE: "RelWithDebInfo" | |
parallelproj: "ON" | |
ROOT: "OFF" | |
ITK: "ON" | |
- os: ubuntu-latest | |
compiler: gcc | |
compiler_version: 12 | |
cuda_version: "12.1.0" | |
BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17" | |
BUILD_TYPE: "Release" | |
parallelproj: "ON" | |
ROOT: "OFF" | |
ITK: "ON" | |
- os: macOS-latest | |
compiler: gcc | |
compiler_version: 11 | |
cuda_version: "0" | |
BUILD_FLAGS: "-DSTIR_OPENMP=OFF" | |
parallelproj: "OFF" | |
BUILD_TYPE: "Debug" | |
ROOT: "OFF" | |
ITK: "OFF" | |
# Currently disabled due to problems with listmode recon, see https://github.com/UCL/STIR/issues/1200 | |
#- os: macOS-latest | |
# compiler: clang | |
# compiler_version: 16 | |
# BUILD_FLAGS: "-DSTIR_OPENMP=OFF" | |
# parallelproj: "OFF" | |
# BUILD_TYPE: "Release" | |
# ROOT: "OFF" | |
# ITK: "OFF" | |
# let's run all of them, as opposed to aborting when one fails | |
fail-fast: false | |
name: ${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }} | |
steps: | |
- name: disk space | |
shell: bash | |
run: | | |
case ${{matrix.os}} in | |
(ubuntu* | macOS*) | |
df -h | |
# saves about 2GB | |
echo removing dotnet | |
sudo rm -rf /usr/share/dotnet | |
# saves about 10 GB | |
echo removing agent_tools | |
sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
# saves about 10 GB | |
echo removing android files | |
sudo rm -rf /usr/local/lib/android | |
df -h | |
;; | |
(windows*) | |
# no idea how to do this | |
;; | |
esac | |
- uses: actions/checkout@v4 | |
with: | |
submodules: recursive | |
- name: disk space | |
shell: bash | |
run: | | |
case ${{matrix.os}} in | |
(ubuntu* | macOS*) | |
sudo .github/workflows/GHA_increase_disk_space.sh | |
;; | |
(windows*) | |
# no idea what to do here | |
;; | |
esac | |
- name: set_compiler_variables | |
shell: bash | |
run: | | |
set -ex | |
if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | |
CC="clang" | |
CXX="clang++" | |
elif test 'XX${{ matrix.compiler }}' = 'XXgcc'; then | |
CC="gcc" | |
CXX="g++" | |
fi | |
if test 'XX${{ matrix.compiler_version }}' != 'XX'; then | |
CC=${CC}-${{ matrix.compiler_version }} | |
CXX=${CXX}-${{ matrix.compiler_version }} | |
fi | |
if test 'XX${{ matrix.os }}' = 'XXmacOS-latest'; then | |
if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | |
brew install llvm@${{ matrix.compiler_version }} | |
if test XX${HOMEBREW_PREFIX} = XX; then | |
HOMEBREW_PREFIX=/usr/local | |
fi | |
LDFLAGS="-L$HOMEBREW_PREFIX/opt/llvm/lib/c++ -Wl,-rpath,$HOMEBREW_PREFIX/opt/llvm/lib/c++" | |
# make available to jobs below | |
echo LDFLAGS="$LDFLAGS" >> $GITHUB_ENV | |
CC="$HOMEBREW_PREFIX/opt/llvm/bin/clang" | |
CXX="$HOMEBREW_PREFIX/opt/llvm/bin/clang++" | |
fi | |
fi | |
export CC CXX | |
# make available to jobs below | |
echo CC="$CC" >> $GITHUB_ENV | |
echo CXX="$CXX" >> $GITHUB_ENV | |
- if: matrix.cuda_version != '0' | |
uses: Jimver/cuda-toolkit@v0.2.11 | |
id: cuda-toolkit | |
with: | |
cuda: ${{ matrix.cuda_version }} | |
linux-local-args: '["--toolkit"]' | |
- name: install_dependencies | |
shell: bash | |
run: | | |
set -ex | |
# We will install some external dependencies here | |
CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install | |
case ${{matrix.os}} in | |
(ubuntu*) | |
sudo apt update | |
# install compiler | |
if test 'XX${{ matrix.compiler }}' = 'XXclang'; then | |
# package is called clang, need libomp-dev for OpenMP support | |
sudo apt install $CC libomp-dev | |
else | |
sudo apt install $CXX | |
fi | |
# other dependencies | |
sudo apt install libboost-dev libhdf5-serial-dev swig python3-dev nlohmann-json3-dev | |
if test "${{matrix.ITK}}XX" == "ONXX"; then | |
sudo apt install libinsighttoolkit5-dev | |
fi | |
# free up some disk space | |
apt autoremove --purge && sudo apt clean | |
PYTHON_EXECUTABLE=$(which python3) | |
;; | |
(macOS*) | |
brew install boost swig python nlohmann-json | |
PYTHON_EXECUTABLE=$(which python3) | |
;; | |
(windows*) | |
# this compiles the whole thing so takes ages | |
vcpkg install boost-core hdf5 nlohmann-json | |
# swig is preinstalled and is currently not in vcpcg | |
vcpkg list | |
PYTHON_EXECUTABLE=$(which python3) | |
;; | |
esac | |
echo PYTHON_EXECUTABLE="$PYTHON_EXECUTABLE" >> $GITHUB_ENV | |
${PYTHON_EXECUTABLE} -m venv ${GITHUB_WORKSPACE}/my-env | |
source ${GITHUB_WORKSPACE}/my-env/bin/activate | |
#python -m pip install -U pip | |
case ${{matrix.os}} in | |
(macOS*) | |
# attempt to get round buggy Accelerate builds, see https://github.com/numpy/numpy/issues/15947 | |
# but it didn't work, so commented out | |
# brew install openblas | |
# export OPENBLAS=$(brew --prefix openblas) | |
#python -m pip install --no-cache-dir --no-binary numpy numpy # avoid the cached .whl! | |
python -m pip install numpy | |
;; | |
(*) | |
python -m pip install numpy | |
;; | |
esac | |
python -m pip install pytest | |
if test "${{matrix.parallelproj}}XX" == "ONXX"; then | |
git clone --depth 1 --branch v1.7.3 https://github.com/gschramm/parallelproj | |
mkdir parallelproj/build | |
cd parallelproj/build | |
if test "${{matrix.cuda_version}}" == "0"; then | |
extra_args="-DSKIP_CUDA_LIB:BOOL=ON" | |
fi | |
cmake .. -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} ${extra_args} | |
cmake --build . --target install --config Release | |
cd ../.. | |
rm -rf parallelproj | |
fi | |
# Install ROOT (warning: currently only valid on Ubuntu) | |
if test "${{matrix.ROOT}}XX" == "ONXX"; then | |
ROOT_file=root_v6.28.12.Linux-ubuntu20-x86_64-gcc9.4.tar.gz | |
wget https://root.cern/download/"$ROOT_file" | |
tar -xzvf "$ROOT_file" | |
rm "$ROOT_file" | |
source root/bin/thisroot.sh | |
fi | |
# we'll install some dependencies with shared libraries, so need to let the OS know | |
# thisroot.sh also modified the path, so save that for the recon_test_pack | |
case ${{matrix.os}} in | |
(ubuntu*) | |
echo LD_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV | |
echo PATH="$PATH" >> $GITHUB_ENV | |
;; | |
(macOS*) | |
echo DYLD_FALLBACK_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$DYLD_FALLBACK_LIBRARY_PATH" >> $GITHUB_ENV | |
echo PATH="$PATH" >> $GITHUB_ENV | |
;; | |
(windows*) | |
echo PATH="${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/bin:$PATH" >> $GITHUB_ENV | |
;; | |
esac | |
- name: ccache | |
uses: hendrikmuhs/ccache-action@v1 | |
with: | |
key: ${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }} | |
max-size: "2G" | |
- name: configure | |
shell: bash | |
env: | |
BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | |
BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }} | |
run: | | |
set -ex | |
source ${GITHUB_WORKSPACE}/my-env/bin/activate | |
#export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH" | |
cmake --version | |
if test "XX$CC" != "XX"; then | |
$CC --version | |
$CXX --version | |
fi | |
CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install | |
# make available to jobs below | |
echo CMAKE_INSTALL_PREFIX="$CMAKE_INSTALL_PREFIX" >> $GITHUB_ENV | |
EXTRA_BUILD_FLAGS="-DBUILD_SWIG_PYTHON=ON -DPYTHON_EXECUTABLE=`which python`" | |
EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DCMAKE_BUILD_TYPE=${BUILD_TYPE}" | |
EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDOWNLOAD_ZENODO_TEST_DATA=ON" | |
EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDISABLE_STIR_LOCAL=OFF -DSTIR_LOCAL=${GITHUB_WORKSPACE}/examples/C++/using_STIR_LOCAL" | |
echo "cmake flags $BUILD_FLAGS $EXTRA_BUILD_FLAGS" | |
mkdir build | |
cd build | |
cmake -S .. ${BUILD_FLAGS} ${EXTRA_BUILD_FLAGS} | |
# report disk space | |
case ${{matrix.os}} in | |
(ubuntu* | macOS*) | |
df -h | |
;; | |
(windows*) | |
# no idea how to do this | |
;; | |
esac | |
- name: build | |
shell: bash | |
env: | |
BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | |
run: | | |
cd ${GITHUB_WORKSPACE}/build; | |
source ${GITHUB_WORKSPACE}/my-env/bin/activate | |
cmake --build . -j 2 --config ${BUILD_TYPE}} --target install | |
# Enable tmate debugging of manually-triggered workflows if the input option was provided | |
- name: Setup tmate session if triggered | |
uses: mxschmitt/action-tmate@v3 | |
timeout-minutes: 15 | |
if: ${{ github.event_name == 'workflow_dispatch' && inputs.debug_enabled == 'true' }} | |
- name: ctest | |
shell: bash | |
env: | |
BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | |
run: | | |
set -vx | |
cd ${GITHUB_WORKSPACE}/build | |
# find test exclusions. Complicated due to need of single -E argument and | pattern | |
if test ${{matrix.cuda_version}} != "0"; then | |
# No CUDA drivers on GitHub Actions | |
EXCLUDE="parallelproj|test_blocks_on_cylindrical_projectors" | |
fi | |
# don't run all of them in Debug mode as it takes too long | |
if test ${BUILD_TYPE} = Debug; then | |
# Also excluding test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeDataWithProjMatrixByBin | |
# as it is a bit slow. Moreover it fails on MacOS (Debug) | |
# https://github.com/UCL/STIR/pull/1418#issuecomment-2109518132 | |
EXCLUDE_Debug="test_data_processor_projectors|test_export_array|test_ArcCorrection|test_PoissonLogLikelihoodWithLinearModelForMeanAndListModeWithProjMatrixByBin" | |
EXCLUDE="${EXCLUDE_Debug}${EXCLUDE:+"|"}${EXCLUDE}" | |
fi | |
# prepend -E | |
if [ ! -z "${EXCLUDE}" ]; then | |
EXCLUDE="-E ${EXCLUDE}" | |
fi | |
# execute tests | |
ctest --output-on-failure -C ${BUILD_TYPE} ${EXCLUDE} | |
- name: Upload ctest log files for debugging | |
uses: actions/upload-artifact@v4 | |
if: failure() | |
with: | |
name: ctest_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }} | |
path: | | |
${{ github.workspace }}/build/**/*.log | |
${{ github.workspace }}/build/**/*.hv | |
${{ github.workspace }}/build/**/*.v | |
${{ github.workspace }}/build/**/*.hs | |
${{ github.workspace }}/build/**/*.s | |
retention-days: 7 | |
- name: C++ examples with STIR_LOCAL | |
shell: bash | |
run: | | |
set -ex; | |
PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH | |
# Run examples to see if they work | |
cd ${GITHUB_WORKSPACE}/examples/PET_simulation | |
./run_simulation.sh 1> /dev/null | |
# Run the Demo executables | |
EXE_LOC=${GITHUB_WORKSPACE}/build/src/examples/C++/using_STIR_LOCAL | |
cd ${GITHUB_WORKSPACE}/examples/C++/using_STIR_LOCAL | |
generate_image generate_image.par | |
forward_project sino.hs image.hv small.hs | |
# Cannot test demo1 or demo2 as they require interactivity. Piping does not work. | |
${EXE_LOC}/demo3 demo.par --display_off | |
${EXE_LOC}/demo3 demoPM.par --display_off | |
${EXE_LOC}/demo4_obj_fun demo4_obj_fun.par | |
${EXE_LOC}/demo5_line_search demo5_line_search.par | |
- name: remove build | |
shell: bash | |
# remove to create some disk space | |
run: | | |
set -x | |
cd ${GITHUB_WORKSPACE} | |
df -h . | |
rm -rf ./build | |
df -h . | |
- name: C++ examples with installed STIR | |
shell: bash | |
run: | | |
set -ex; | |
# build and run C++/using_installed_STIR | |
PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH | |
cd ${GITHUB_WORKSPACE}/examples/C++/using_installed_STIR | |
cmake -S . -B build/ -DCMAKE_INSTALL_PREFIX:PATH=${CMAKE_INSTALL_PREFIX} | |
cmake --build build/ --config Release --target install | |
# run demo | |
demo_create_image | |
# just check if its output makes sense | |
list_image_info test.hv | |
rm -rf build | |
- name: recon_test_pack | |
shell: bash | |
env: | |
BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }} | |
BUILD_TYPE: ${{ matrix.BUILD_TYPE }} | |
run: | | |
set -ex; | |
PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH | |
cd ${GITHUB_WORKSPACE}/recon_test_pack | |
./run_tests.sh --nointbp | |
# don't run all of them in Debug mode as it takes too long | |
if test ${BUILD_TYPE} != Debug; then | |
./run_test_simulate_and_recon.sh | |
./run_test_listmode_recon.sh | |
./run_test_simulate_and_recon_with_motion.sh | |
./run_scatter_tests.sh | |
./run_test_zoom_image.sh | |
./run_ML_norm_tests.sh | |
if test "${{matrix.ROOT}}XX" == "ONXX"; then ./run_root_GATE.sh; fi | |
./run_tests_modelling.sh | |
cd ${GITHUB_WORKSPACE}/recon_test_pack/SPECT | |
./run_SPECT_tests.sh | |
fi | |
- name: Upload recon_test_pack log files for debugging | |
uses: actions/upload-artifact@v4 | |
if: failure() | |
with: | |
name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }} | |
path: | | |
${{ github.workspace }}/recon_test_pack/**/*.log | |
${{ github.workspace }}/recon_test_pack/**/my_*v | |
${{ github.workspace }}/recon_test_pack/**/my_*s | |
retention-days: 7 | |
- name: remove recon_test_pack | |
shell: bash | |
run: | | |
rm -rf ${GITHUB_WORKSPACE}/recon_test_pack | |
- name: Python | |
shell: bash | |
run: | | |
set -ex | |
source ${GITHUB_WORKSPACE}/my-env/bin/activate | |
# Run Python tests, making sure we're using the correct Python interpreter | |
which python | |
export PYTHONPATH=${CMAKE_INSTALL_PREFIX}/python | |
cd ${GITHUB_WORKSPACE}/src | |
case ${{matrix.os}} in | |
(macOS*) | |
echo skipping pytest due to numpy problem for now. | |
;; | |
(*) | |
python -m pytest . | |
;; | |
esac |