Merge pull request #2514 from boutproject/ci-cmake-only

Switch to CMake in CI and docs
boutproject · Jun 14, 2023 · f695441 · f695441
2 parents 3c06094 + 23f8939
commit f695441
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Showing 20 changed files with 244 additions and 303 deletions.
diff --git a/.ci_fedora.sh b/.ci_fedora.sh
@@ -58,7 +58,7 @@ else
     cd
     cd BOUT-dev
     echo "starting configure"
-    time cmake -DBOUT_USE_PETSC=ON -S . -B build
+    time cmake -S . -B build -DBOUT_USE_PETSC=ON
     time make -C build build-check -j 2
     time make -C build check
 fi
diff --git a/.ci_with_cmake.sh b/.ci_with_cmake.sh
@@ -3,13 +3,23 @@
 set -ex
 
 cmake --version
-cmake . -B build $@ -DCMAKE_INSTALL_PREFIX=$(pwd)/installed
+cmake -S . -B build $@ -DCMAKE_INSTALL_PREFIX=$(pwd)/installed
+
+if test ".$UNIT_ONLY" = ".YES" ; then
+    make -C build build-check-unit-tests
+    make -C build check-unit-tests
+    exit 0
+fi
+
 cmake --build build --target build-check -j 2
 cd build
 ctest --output-on-failure --timeout 300
 
+export LD_LIBRARY_PATH=/home/runner/local/lib:$LD_LIBRARY_PATH
+
 # Test bout-config basic functionallity
 cd ../examples/make-script
+PATH=../../build/bin:$PATH bout-config --all
 PATH=../../build/bin:$PATH make
 ./test --help
 cd -
@@ -25,6 +35,7 @@ rm -rf build
 # Test installation with plain `make`
 cd ../examples/make-script
 rm test
+PATH=../../installed/bin:$PATH bout-config --all
 PATH=../../installed/bin:$PATH make
 ./test --help
 cd -

diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -25,45 +25,42 @@ jobs:
       OMPI_MCA_rmaps_base_oversubscribe: yes
       MPIRUN: mpiexec -np
     strategy:
-      fail-fast: false
+      fail-fast: true
       matrix:
         # Need this to be able to exclude the coverage job
         is_master_or_next:
           - ${{ github.ref ==  'refs/heads/master' || github.ref == 'refs/heads/next'  || github.base_ref ==  'master' || github.base_ref == 'next' }}
         config:
           - name: "Default options, Ubuntu 20.04"
             os: ubuntu-20.04
-            configure_options: ""
-            script_flags: "-uim"
+            cmake_options: ""
 
-          - name: "Optimised, shared, Python"
+          - name: "Optimised, static"
             os: ubuntu-20.04
-            configure_options: "--enable-shared
-                                --enable-checks=no
-                                --enable-optimize=3
-                                --disable-signal
-                                --disable-track
-                                --disable-backtrace
-                                --with-petsc
-                                --with-slepc
-                                --with-sundials=/home/runner/local"
-            script_flags: "-uim -t shared -t python"
-            omp_num_threads: 1
+            cmake_options: "-DBOUT_ENABLE_CHECKS=OFF
+                            -DBUILD_SHARED_LIBS=OFF
+                            -DCXXFLAGS=-Ofast
+                            -DBOUT_ENABLE_SIGNAL=OFF
+                            -DBOUT_ENABLE_TRACK=OFF
+                            -DBOUT_ENABLE_BACKTRACE=OFF
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DSUNDIALS_ROOT=/home/runner/local"
 
           - name: "Debug, shared"
             os: ubuntu-20.04
-            configure_options: "--enable-shared
-                                --enable-sigfpe
-                                --enable-debug
-                                --enable-track
-                                --with-petsc
-                                --with-slepc
-                                --with-sundials=/home/runner/local"
-            script_flags: "-uim"
-            omp_num_threads: 1
-
-          - name: "CMake, shared, release"
-            os: ubuntu-latest
+            cmake_options: "-DBOUT_ENABLE_CHECKS=3
+                            -DCMAKE_BUILD_TYPE=Debug
+                            -DBOUT_ENABLE_SIGNAL=ON
+                            -DBOUT_ENABLE_TRACK=ON
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DSUNDIALS_ROOT=/home/runner/local"
+
+          - name: "Shared, release, Ubuntu 20.04"
+            os: ubuntu-20.04
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_OPENMP=ON
                             -DCMAKE_BUILD_TYPE=Release
@@ -74,7 +71,7 @@ jobs:
                             -DSUNDIALS_ROOT=/home/runner/local"
             omp_num_threads: 2
 
-          - name: "CMake, shared, OpenMP, 3D metrics"
+          - name: "Shared, OpenMP, 3D metrics"
             os: ubuntu-latest
             cmake_options: "-DBUILD_SHARED_LIBS=ON
                             -DBOUT_ENABLE_METRIC_3D=ON
@@ -88,16 +85,17 @@ jobs:
 
           - name: "Coverage"
             os: ubuntu-20.04
-            configure_options: "--enable-shared
-                                --enable-code-coverage
-                                --enable-debug
-                                --enable-track
-                                --with-lapack
-                                --with-petsc
-                                --with-slepc
-                                --with-sundials=/home/runner/local"
-            omp_num_threads: 1
-            script_flags: "-u"
+            cmake_options: "-DBUILD_SHARED_LIBS=ON
+                            -DCMAKE_BUILD_TYPE=Debug
+                            -DCHECK=3
+                            -DENABLE_COVERAGE=ON
+                            -DBOUT_USE_PETSC=ON
+                            -DBOUT_USE_SLEPC=ON
+                            -DBOUT_USE_HDF5=ON
+                            -DBOUT_USE_SUNDIALS=ON
+                            -DBOUT_ENABLE_PYTHON=ON
+                            -DSUNDIALS_ROOT=/home/runner/local"
+            unit_only: YES
         exclude:
           # Don't run the coverage tests if the branch isn't master or next
           - is_master_or_next: false
@@ -108,7 +106,6 @@ jobs:
       - name: Job information
         run: |
           echo Build: ${{ matrix.config.name }}, ${{ matrix.config.os }}
-          echo Configure options: ${{ matrix.config.configure_options }}
           echo CMake options: ${{ matrix.config.cmake_options }}
 
       - name: Install dependencies
@@ -137,7 +134,7 @@ jobs:
 
       - name: Install pip packages
         run: |
-          ./.pip_install_for_ci.sh 'cython~=0.29' 'netcdf4~=1.5' 'sympy~=1.5' 'gcovr' 'cmake' 'h5py' zoidberg
+          ./.pip_install_for_ci.sh 'cython~=0.29' 'netcdf4~=1.5' 'sympy~=1.5' 'gcovr' 'cmake' 'h5py' zoidberg fastcov
           # Add the pip install location to the runner's PATH
           echo ~/.local/bin >> $GITHUB_PATH
 
@@ -150,16 +147,8 @@ jobs:
       - name: Build SUNDIALS
         run: ./.build_sundials_for_ci.sh
 
-      - name: Build (configure)
-        if: ${{ ! contains(matrix.config.name, 'CMake') }}
-        run: ./.ci_script.sh ${{ matrix.config.script_flags }}
-        env:
-          LD_LIBRARY_PATH: /home/runner/local/lib:$LD_LIBRARY_PATH
-          CONFIGURE_OPTIONS: ${{ matrix.config.configure_options }}
-
       - name: Build (CMake)
-        if: ${{ contains(matrix.config.name, 'CMake') }}
-        run: ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
+        run: UNIT_ONLY=${{ matrix.config.unit_only }} ./.ci_with_cmake.sh ${{ matrix.config.cmake_options }}
 
       - name: Capture coverage
         if: ${{ matrix.config.name == 'Coverage' }}
@@ -171,7 +160,7 @@ jobs:
           # This is to try and make the coverage report slightly more accurate
           # It still won't include, e.g. any solvers we don't build with though
           find . -name "*.gcno" -exec sh -c 'touch -a "${1%.gcno}.gcda"' _ {} \;
-          make code-coverage-capture
+          make -C build code-coverage-capture
 
       - name: Upload coverage
         if: ${{ matrix.config.name == 'Coverage' }}

diff --git a/.gitignore b/.gitignore
@@ -69,6 +69,9 @@ src/fmt/format.cxx
 /tests/integrated/test-options-netcdf/time.nc
 /tests/integrated/test-yupdown-weights/test_yupdown_weights
 
+coverage.info
+coverage/
+
 # Potential user build directories
 /build/
 /build*/
@@ -78,4 +81,5 @@ src/fmt/format.cxx
 # Python stuff
 /_wheel*/
 /dist/
+/manual/sphinx/_build
 /_version.txt
diff --git a/cmake/FindSUNDIALS.cmake b/cmake/FindSUNDIALS.cmake
@@ -31,10 +31,6 @@
 
 include(FindPackageHandleStandardArgs)
 
-find_package(SUNDIALS CONFIG QUIET)
-if (SUNDIALS_FOUND)
-  return()
-endif()
 
 find_path(SUNDIALS_INCLUDE_DIR
   sundials_config.h

diff --git a/cmake/Sanitizers.cmake b/cmake/Sanitizers.cmake
@@ -10,24 +10,22 @@ function(enable_sanitizers target_name)
 
     if(ENABLE_COVERAGE)
       target_compile_options(${target_name} PUBLIC --coverage -O0 -g)
-      target_link_libraries(${target_name} PUBLIC --coverage)
+      target_link_libraries(${target_name} PUBLIC --coverage -lgcov)
 
-      find_program(fastcov_FOUND fastcov)
-      message(STATUS "Looking for fastcov: ${fastcov_FOUND}")
+      find_program(lcov_FOUND lcov)
+      message(STATUS "Looking for lcov: ${lcov_FOUND}")
       find_program(genhtml_FOUND genhtml)
-      message(STATUS "Looking for genhtml: ${fastcov_FOUND}")
+      message(STATUS "Looking for genhtml: ${genhtml_FOUND}")
 
-      if (fastcov_FOUND AND genhtml_FOUND)
+      if (lcov_FOUND AND genhtml_FOUND)
         set(COVERAGE_NAME coverage CACHE STRING "Name of coverage output file")
         set(COVERAGE_FILE "${COVERAGE_NAME}.info")
         set(COVERAGE_MSG "Open file://${PROJECT_SOURCE_DIR}/${COVERAGE_NAME}/index.html in your browser to view coverage HTML output")
 
         add_custom_target(code-coverage-capture
           COMMAND
-            fastcov --include "${CMAKE_CURRENT_SOURCE_DIR}/src" "${CMAKE_CURRENT_SOURCE_DIR}/include"
-            --exclude "${CMAKE_CURRENT_SOURCE_DIR}/externalpackages"
-            --lcov --process-gcno
-            --output "${COVERAGE_FILE}"
+            lcov -c --directory  "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/bout++.dir/src"
+              --output-file "${COVERAGE_FILE}"
           COMMAND
             genhtml --output-directory "${COVERAGE_NAME}" --demangle-cpp --legend --show-details "${COVERAGE_FILE}"
           COMMAND
@@ -41,11 +39,11 @@ function(enable_sanitizers target_name)
 
         add_custom_target(code-coverage-clean
           COMMAND
-          fastcov --zerocounters
+          lcov --zerocounters
           COMMENT "Cleaning coverage information"
           )
       else()
-        message(STATUS "Coverage enabled, but coverage-capture not available. Please install fastcov and lcov")
+        message(FATAL_ERROR "Coverage enabled, but coverage-capture not available. Please install lcov")
       endif()
 
     endif()

diff --git a/cmake/SetupBOUTThirdParty.cmake b/cmake/SetupBOUTThirdParty.cmake
@@ -81,7 +81,7 @@ if (BOUT_USE_PETSC)
     find_package(PETSc REQUIRED)
     target_link_libraries(bout++ PUBLIC PETSc::PETSc)
     string(JOIN " " CONFIG_PETSC_LIBRARIES ${PETSC_LIBRARIES})
-    set(CONFIG_LDFLAGS "${CONFIG_PETSC_LIBRARIES} ${CONFIG_LDFLAGS}")
+    set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${CONFIG_PETSC_LIBRARIES}")
     foreach(PETSC_INCLUDE ${PETSC_INCLUDES})
       set(CONFIG_CFLAGS "${CONFIG_CFLAGS} -I${PETSC_INCLUDE}")
     endforeach()
@@ -169,7 +169,12 @@ if (BOUT_USE_NETCDF)
     FetchContent_MakeAvailable(netcdf-cxx4)
   else()
     find_package(netCDFCxx REQUIRED)
-    set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${netCDF_CXX_LIBRARY} ${netCDF_LIBRARIES}")
+    foreach(FLAG ${netCDF_CXX_LIBRARY} ${netCDF_LIBRARIES})
+      if("${FLAG}" STREQUAL "netcdf")
+	    set(FLAG -lnetcdf)
+      endif()
+      set(CONFIG_LDFLAGS "${CONFIG_LDFLAGS} ${FLAG}")
+    endforeach()
   endif()
   target_link_libraries(bout++ PUBLIC netCDF::netcdf-cxx4)
 endif()

diff --git a/manual/RELEASE_HOWTO.md b/manual/RELEASE_HOWTO.md
@@ -55,7 +55,6 @@ Before merging PR:
 
 After PR is merged:
 
-- [ ] Make tarball: `./configure && make dist`
 - [ ] Try to summarise the changes!
 - [ ] Make [GitHub Release][gh_release], include change summary **NB:** tag should have
       leading `v`
@@ -73,6 +72,7 @@ After PR is merged:
     - [ ]  [`manual/doxygen/Doxyfile`][Doxyfile]: `PROJECT_NUMBER`
     - [ ]  [`CMakeLists.txt`][CMakeLists]: `_bout_previous_version`, `_bout_next_version`
     - [ ]  [`tools/pylib/_boutpp_build/backend.py`][backend.py]: `_bout_previous_version`, `_bout_next_version`
+- [ ] Make tarball: `cmake -S . -B build && make dist -C build`
 
 [Doxyfile]: ../manual/doxygen/Doxyfile
 [Doxyfile_readthedocs]: ../manual/doxygen/Doxyfile_readthedocs

diff --git a/manual/sphinx/developer_docs/data_types.rst b/manual/sphinx/developer_docs/data_types.rst
@@ -347,7 +347,7 @@ offsets there is a function ``offset(x,y,z)`` so that
 Note that by default no bounds checking is performed. If the checking
 level is increased to 3 or above then bounds checks will be
 performed. This will have a significant (bad) impact on performance, so is
-just for debugging purposes. Configure with ``--enable-checks=3``
+just for debugging purposes. Configure with ``-DCHECK=3``
 option to do this.
 
 

diff --git a/manual/sphinx/developer_docs/mesh.rst b/manual/sphinx/developer_docs/mesh.rst
@@ -263,7 +263,7 @@ The mesh spacing is given by the public members `Coordinates::dx`,
     Field2D zlength();   // Computed from dz
 
 `Coordinates::FieldMetric` can be either `Field2D` or if BOUT++ has
-been configured with ``--enable-metric-3d`` then a `Field3D`.
+been configured with ``-DBOUT_ENABLE_METRIC_3D`` then a `Field3D`.
 
 Metrics
 -------

diff --git a/manual/sphinx/developer_docs/performance_profiling.rst b/manual/sphinx/developer_docs/performance_profiling.rst
@@ -82,11 +82,10 @@ percent of runtime.
 Configure and build
 ~~~~~~~~~~~~~~~~~~~
 
-Configure with ``--with-scorep`` to enable Scorep instrumentation, then build
-as normal.  This option can be combined with other options, but it is usually
-desirable to profile the optimized code, configuring with the flags
-``--enable-optimize=3 --enable-checks=0``. Build the code with ``make`` as
-normal.
+Configure with ``-BOUT_USE_SCOREP`` to enable Scorep instrumentation,
+then build as normal.  This option can be combined with other options,
+but it is usually desirable to profile the optimized code, configuring
+with the flags ````. Build the code with ``make`` as normal.
 
 With CMake:
 
@@ -95,6 +94,7 @@ With CMake:
     $ SCOREP_WRAPPER=off cmake \
       -DCMAKE_C_COMPILER=scorep-mpicc \
       -DCMAKE_CXX_COMPILER=scorep-mpicxx \
+      -DCMAKE_CXX_FLAGS=-O3 -DCHECK=0 \
       <other CMake options>
 
 This will turn off the instrumentation during the configure