Implement a region calculus

.github/ci/spack-envs/gcc7_py36_ompi_h5_ad1_ad2/spack.yaml

@@ -0,0 +1,61 @@
+# This is a Spack environment file.
+#
+# Activating and installing this environment will provide all dependencies
+# that are needed for full-feature development.
+#   https//spack.readthedocs.io/en/latest/environments.html#anonymous-environments
+#
+spack:
+  specs:
+  - adios
+  - adios2
+  - hdf5
+  - openmpi
+
+  packages:
+    adios:
+      variants: ~zfp ~sz ~lz4 ~blosc
+    adios2:
+      variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
+    cmake:
+      externals:
+      - spec: "cmake"
+        prefix: /usr
+      buildable: False
+    openmpi:
+      externals:
+      - spec: "openmpi"
+        prefix: /usr
+      buildable: False
+    perl:
+      externals:
+      - spec: "perl"
+        prefix: /usr
+      buildable: False
+    python:
+      externals:
+      - spec: "python"
+        prefix: /usr
+      buildable: False
+    all:
+      target: ['x86_64']
+      variants: ~fortran
+      compiler: [[email protected]]
+
+  compilers:
+  - compiler:
+      environment: {}
+      extra_rpaths: []
+      flags: {}
+      modules: []
+      operating_system: ubuntu18.04
+      paths:
+        cc: /usr/bin/gcc-7
+        cxx: /usr/bin/g++-7
+        f77: /usr/bin/gfortran
+        fc: /usr/bin/gfortran
+      spec: [email protected]
+      target: x86_64
+
+  config:
+    build_jobs: 2
+

.github/workflows/unix.yml

@@ -17,13 +17,15 @@ jobs:
         sudo .github/workflows/dependencies/install_spack
     - name: Build
       env: {CC: clang, CXX: clang++, CXXFLAGS: -Wno-deprecated-declarations}
+      # The main openPMD code base leads to many clang-tidy warnings
+      # when C++17 is enabled. We cannot enable it yet.
       run: |
         eval $(spack env activate --sh .github/ci/spack-envs/clangtidy_nopy_ompi_h5_ad1_ad2/)
         spack install
 
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DCMAKE_CXX_CLANG_TIDY="$(which clang-tidy);-system-headers=0" -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DCMAKE_BUILD_TYPE=RelWithDebInfo -DCMAKE_CXX_CLANG_TIDY="$(which clang-tidy);-system-headers=0" -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2 2> clang-tidy.log
         cat clang-tidy.log
         if [[ $(wc -m <clang-tidy.log) -gt 1 ]]; then exit 1; fi
@@ -52,7 +54,7 @@ jobs:
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
         export LDFLAGS="${LDFLAGS} -fsanitize=address,undefined -shared-libsan"
         CXXFLAGS="${CXXFLAGS} -fsanitize=address,undefined -shared-libsan"
-        CXXFLAGS="${CXXFLAGS}" cmake -S .. -B . -DopenPMD_USE_MPI=ON -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_ADIOS1=ON -DopenPMD_USE_INVASIVE_TESTS=ON -DCMAKE_VERBOSE_MAKEFILE=ON
+        CXXFLAGS="${CXXFLAGS}" cmake -S .. -B . -DCMAKE_BUILD_TYPE=RelWithDebInfo -DopenPMD_USE_MPI=ON -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_ADIOS1=ON -DopenPMD_USE_INVASIVE_TESTS=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DopenPMD_CXX_STANDARD=17
         cmake --build . --parallel 2
         export ASAN_OPTIONS=detect_stack_use_after_return=1:detect_leaks=1:check_initialization_order=true:strict_init_order=true:detect_stack_use_after_scope=1:fast_unwind_on_malloc=0
         export LSAN_OPTIONS=suppressions="$SOURCEPATH/.github/ci/sanitizer/clang/Leak.supp"
@@ -73,13 +75,14 @@ jobs:
         sudo .github/workflows/dependencies/install_spack
     - name: Build
       env: {CC: clang-5.0, CXX: clang++-5.0, CXXFLAGS: -Werror -Wno-deprecated-declarations}
+      # Clang 5 does not handle GCC 10's STL in C++17-mode
       run: |
         eval $(spack env activate --sh .github/ci/spack-envs/clang5_nopy_nompi_h5/)
         spack install
 
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=OFF -DopenPMD_USE_MPI=OFF -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DCMAKE_BUILD_TYPE=RelWithDebInfo -DopenPMD_USE_PYTHON=OFF -DopenPMD_USE_MPI=OFF -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -97,13 +100,14 @@ jobs:
         sudo .github/workflows/dependencies/install_spack
     - name: Build
       env: {CC: clang-5.0, CXX: clang++-5.0, CXXFLAGS: -Werror -Wno-deprecated-declarations}
+      # Clang 5 does not handle GCC 10's STL in C++17-mode
       run: |
         eval $(spack env activate --sh .github/ci/spack-envs/clang5_nopy_ompi_h5_ad1_ad2_bp3/)
         spack install
 
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=OFF -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS1=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DCMAKE_BUILD_TYPE=RelWithDebInfo -DopenPMD_USE_PYTHON=OFF -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS1=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -126,13 +130,14 @@ jobs:
         sudo .github/workflows/dependencies/install_spack
     - name: Build
       env: {CC: clang-5.0, CXX: clang++-5.0, CXXFLAGS: -Werror -Wno-deprecated-declarations}
+      # Clang 5 does not handle GCC 10's STL in C++17-mode
       run: |
         eval $(spack env activate --sh .github/ci/spack-envs/clang5_nopy_ompi_h5_ad1_ad2_bp3/)
         spack install
 
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=OFF -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS1=OFF -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DCMAKE_BUILD_TYPE=RelWithDebInfo -DopenPMD_USE_PYTHON=OFF -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS1=OFF -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         export OPENPMD2_ADIOS2_SCHEMA=20210209
         ctest --output-on-failure
@@ -158,7 +163,7 @@ jobs:
       run: |
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=OFF -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON -DCMAKE_VERBOSE_MAKEFILE=ON
+        cmake -S .. -B . -DCMAKE_BUILD_TYPE=RelWithDebInfo -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=OFF -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DopenPMD_CXX_STANDARD=17
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -192,7 +197,7 @@ jobs:
       run: |
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DCMAKE_BUILD_TYPE=RelWithDebInfo -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_ADIOS2=ON -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -213,7 +218,7 @@ jobs:
     - uses: actions/checkout@v2
     - name: Spack Cache
       uses: actions/cache@v2
-      with: {path: /opt/spack, key: gcc5_py36_ompi_h5_ad1_ad2 }
+      with: {path: /opt/spack, key: gcc7_py36_ompi_h5_ad1_ad2 }
     - name: Install
       run: |
         sudo apt-get update
@@ -226,14 +231,15 @@ jobs:
         python3 -m pip install -U dask
         python3 -m pip install -U pyarrow
     - name: Build
-      env: {CC: gcc-5, CXX: g++-5, CXXFLAGS: -Werror -Wno-deprecated-declarations}
+      env: {CC: gcc-7, CXX: g++-7, CXXFLAGS: -Werror -Wno-deprecated-declarations}
       run: |
-        eval $(spack env activate --sh .github/ci/spack-envs/gcc5_py36_ompi_h5_ad1_ad2/)
+        eval $(spack env activate --sh .github/ci/spack-envs/gcc7_py36_ompi_h5_ad1_ad2/)
         spack install
 
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
         cmake -S .. -B . \
+          -DCMAKE_BUILD_TYPE=RelWithDebInfo \
           -DopenPMD_USE_PYTHON=ON \
           -DopenPMD_USE_MPI=ON    \
           -DopenPMD_USE_HDF5=ON   \
@@ -257,7 +263,7 @@ jobs:
       run: |
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
-        cmake -S .. -B . -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON
+        cmake -S .. -B . -DCMAKE_BUILD_TYPE=RelWithDebInfo -DopenPMD_USE_PYTHON=ON -DopenPMD_USE_MPI=ON -DopenPMD_USE_HDF5=ON -DopenPMD_USE_INVASIVE_TESTS=ON -DopenPMD_CXX_STANDARD=17
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -304,11 +310,14 @@ jobs:
         sudo .github/workflows/dependencies/install_icc
     - name: Build
       env: {CXXFLAGS: -Werror -Wno-deprecated-declarations}
+      # C++17 not properly supported (false positives for unused
+      # arguments and missing return statements with `if constexpr`)
       run: |
         set +e; source /opt/intel/oneapi/setvars.sh; set -e
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
         cmake -S .. -B . \
+          -DCMAKE_BUILD_TYPE=RelWithDebInfo  \
           -DCMAKE_C_COMPILER=$(which icc)    \
           -DCMAKE_CXX_COMPILER=$(which icpc) \
           -DopenPMD_USE_PYTHON=OFF           \
@@ -330,6 +339,7 @@ jobs:
         mkdir build && cd build
         ../share/openPMD/download_samples.sh && chmod u-w samples/git-sample/*.h5
         cmake -S .. -B . \
+          -DCMAKE_BUILD_TYPE=RelWithDebInfo  \
           -DCMAKE_C_COMPILER=$(which icx)    \
           -DCMAKE_CXX_COMPILER=$(which icpx) \
           -DopenPMD_USE_PYTHON=OFF           \
@@ -339,6 +349,7 @@ jobs:
           -DCMAKE_C_STANDARD_COMPUTED_DEFAULT="11"       \
           -DCMAKE_CXX_COMPILER_ID="Clang"                \
           -DCMAKE_CXX_COMPILER_VERSION=12.0              \
-          -DCMAKE_CXX_STANDARD_COMPUTED_DEFAULT="14"
+          -DCMAKE_CXX_STANDARD_COMPUTED_DEFAULT="17"     \
+          -DopenPMD_CXX_STANDARD=17
         cmake --build . --parallel 2
         ctest --output-on-failure

CMakeLists.txt

@@ -69,6 +69,7 @@ openpmd_option(ADIOS1         "ADIOS1 backend (.bp files)"                AUTO)
 openpmd_option(ADIOS2         "ADIOS2 backend (.bp files)"                AUTO)
 openpmd_option(PYTHON         "Enable Python bindings"                    AUTO)
 
+option(openPMD_CXX_STANDARD          "Which C++ standard to use (14 or 17)" OFF)
 option(openPMD_INSTALL               "Add installation targets"             ON)
 option(openPMD_HAVE_PKGCONFIG        "Generate a .pc file for pkg-config"   ON)
 option(openPMD_USE_INTERNAL_VARIANT  "Use internally shipped MPark.Variant" ON)
@@ -79,6 +80,17 @@ option(openPMD_USE_INTERNAL_JSON     "Use internally shipped nlohmann-json" ON)
 option(openPMD_USE_INVASIVE_TESTS "Enable unit tests that modify source code" OFF)
 option(openPMD_USE_VERIFY "Enable internal VERIFY (assert) macro independent of build type" ON)
 
+if(NOT openPMD_CXX_STANDARD)
+    set(openPMD_CXX_STANDARD 14)
+endif()
+if(openPMD_CXX_STANDARD STREQUAL 14)
+    set(openPMD_CXX_STD cxx_std_14)
+elseif(openPMD_CXX_STANDARD STREQUAL 17)
+    set(openPMD_CXX_STD cxx_std_17)
+else()
+    message(FATAL_ERROR "openPMD_CXX_STANDARD must be either 14 or 17; found ${openPMD_CXX_STANDARD}")
+endif()
+
 set(CMAKE_CONFIGURATION_TYPES "Release;Debug;MinSizeRel;RelWithDebInfo")
 if(NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE "Release" CACHE STRING
@@ -396,9 +408,10 @@ add_library(openPMD::openPMD ALIAS openPMD)
 
 # properties
 target_compile_features(openPMD
-    PUBLIC cxx_std_14
+    PUBLIC ${openPMD_CXX_STD}
 )
 set_target_properties(openPMD PROPERTIES
+    CXX_STANDARD ${openPMD_CXX_STANDARD}
     CXX_EXTENSIONS OFF
     CXX_STANDARD_REQUIRED ON
     POSITION_INDEPENDENT_CODE ON
@@ -475,10 +488,10 @@ if(openPMD_HAVE_ADIOS1)
     add_library(openPMD.ADIOS1.Serial SHARED ${IO_ADIOS1_SEQUENTIAL_SOURCE})
     add_library(openPMD.ADIOS1.Parallel SHARED ${IO_ADIOS1_SOURCE})
     target_compile_features(openPMD.ADIOS1.Serial
-        PUBLIC cxx_std_14
+        PUBLIC ${openPMD_CXX_STD}
     )
     target_compile_features(openPMD.ADIOS1.Parallel
-        PUBLIC cxx_std_14
+        PUBLIC ${openPMD_CXX_STD}
     )
     target_compile_options(openPMD.ADIOS1.Serial PUBLIC ${_msvc_options})
     target_compile_options(openPMD.ADIOS1.Parallel PUBLIC ${_msvc_options})
@@ -498,6 +511,7 @@ if(openPMD_HAVE_ADIOS1)
     endif()
 
     set_target_properties(openPMD.ADIOS1.Serial PROPERTIES
+        CXX_STANDARD ${openPMD_CXX_STANDARD}
         CXX_EXTENSIONS OFF
         CXX_STANDARD_REQUIRED ON
         POSITION_INDEPENDENT_CODE ON
@@ -525,6 +539,7 @@ if(openPMD_HAVE_ADIOS1)
 
     if(openPMD_HAVE_MPI)
         set_target_properties(openPMD.ADIOS1.Parallel PROPERTIES
+            CXX_STANDARD ${openPMD_CXX_STANDARD}
             CXX_EXTENSIONS OFF
             CXX_STANDARD_REQUIRED ON
             POSITION_INDEPENDENT_CODE ON
@@ -685,6 +700,13 @@ set(openPMD_TEST_NAMES
     SerialIO
     ParallelIO
 )
+if(openPMD_CXX_STANDARD STREQUAL 17)
+    list(APPEND openPMD_TEST_NAMES
+        RegionsBox
+        RegionsPoint
+        RegionsRegion
+    )
+endif()
 # command line tools
 set(openPMD_CLI_TOOL_NAMES
     ls
@@ -711,6 +733,11 @@ set(openPMD_EXAMPLE_NAMES
     10_streaming_read
     12_span_write
 )
+if(openPMD_CXX_STANDARD STREQUAL 17)
+    list(APPEND openPMD_EXAMPLE_NAMES
+        13_regions
+    )
+endif()
 set(openPMD_PYTHON_EXAMPLE_NAMES
     2_read_serial
     2a_read_thetaMode_serial
@@ -737,9 +764,10 @@ if(openPMD_BUILD_TESTING)
         test/CatchRunner.cpp)  # Always MPI_Init with Serial Fallback
     add_library(CatchMain   ${_openpmd_lib_type}
         test/CatchMain.cpp)    # Serial only
-    target_compile_features(CatchRunner PUBLIC cxx_std_14)
-    target_compile_features(CatchMain   PUBLIC cxx_std_14)
+    target_compile_features(CatchRunner PUBLIC ${openPMD_CXX_STD})
+    target_compile_features(CatchMain   PUBLIC ${openPMD_CXX_STD})
     set_target_properties(CatchRunner CatchMain PROPERTIES
+        CXX_STANDARD ${openPMD_CXX_STANDARD}
         CXX_EXTENSIONS OFF
         CXX_STANDARD_REQUIRED ON
         POSITION_INDEPENDENT_CODE ON
@@ -766,6 +794,12 @@ if(openPMD_BUILD_TESTING)
         else()
             target_link_libraries(${testname}Tests PRIVATE CatchMain)
         endif()
+        target_compile_features(${testname}Tests PUBLIC ${openPMD_CXX_STD})
+        set_target_properties(${testname}Tests PROPERTIES
+            CXX_STANDARD ${openPMD_CXX_STANDARD}
+            CXX_EXTENSIONS OFF
+            CXX_STANDARD_REQUIRED ON
+        )
     endforeach()
 endif()
 
@@ -782,10 +816,22 @@ if(openPMD_BUILD_EXAMPLES)
             if(openPMD_HAVE_MPI)
                 add_executable(${examplename} examples/${examplename}.cpp)
                 target_link_libraries(${examplename} PRIVATE openPMD)
+                target_compile_features(${examplename} PUBLIC ${openPMD_CXX_STD})
+                set_target_properties(${examplename} PROPERTIES
+                    CXX_STANDARD ${openPMD_CXX_STANDARD}
+                    CXX_EXTENSIONS OFF
+                    CXX_STANDARD_REQUIRED ON
+                )
             endif()
         else()
             add_executable(${examplename} examples/${examplename}.cpp)
             target_link_libraries(${examplename} PRIVATE openPMD)
+            target_compile_features(${examplename} PUBLIC ${openPMD_CXX_STD})
+            set_target_properties(${examplename} PROPERTIES
+                CXX_STANDARD ${openPMD_CXX_STANDARD}
+                CXX_EXTENSIONS OFF
+                CXX_STANDARD_REQUIRED ON
+            )
         endif()
     endforeach()
 endif()
@@ -1309,6 +1355,7 @@ else()
     message("  Installation: OFF")
 endif()
 message("")
+message("  C++ standard: ${openPMD_CXX_STD}")
 message("  Build Type: ${CMAKE_BUILD_TYPE}")
 if(openPMD_BUILD_SHARED_LIBS)
     message("  Library: shared")