Implement a region calculus

.appveyor.yml

@@ -121,7 +121,7 @@ before_build:
 #  - cmd: if "%TARGET_ARCH%"=="x64" "C:\Program Files (x86)\Microsoft Visual Studio 15.9\VC\vcvarsall.bat" amd64
 
   # CMake configure
-  - cmd: cmake -G "%OPENPMD_CMAKE_GENERATOR%" -DCMAKE_BUILD_TYPE=%CONFIGURATION% -DBUILD_SHARED_LIBS=%SHARED% -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX="%CONDA_INSTALL_LOCN%" -DCMAKE_INSTALL_BINDIR="Library\bin" ".."
+  - cmd: cmake -G "%OPENPMD_CMAKE_GENERATOR%" -DopenPMD_USE_REGIONS=OFF -DCMAKE_BUILD_TYPE=%CONFIGURATION% -DBUILD_SHARED_LIBS=%SHARED% -DBUILD_TESTING=ON -DCMAKE_INSTALL_PREFIX="%CONDA_INSTALL_LOCN%" -DCMAKE_INSTALL_BINDIR="Library\bin" ".."
 
 build_script:
   - cmd: cmake --build . --config %CONFIGURATION%

.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
@@ -58,6 +60,7 @@ jobs:
           -DopenPMD_USE_HDF5=ON           \
           -DopenPMD_USE_ADIOS2=ON         \
           -DopenPMD_USE_ADIOS1=ON         \
+          -DopenPMD_USE_REGIONS=ON        \
           -DopenPMD_USE_INVASIVE_TESTS=ON \
           -DCMAKE_VERBOSE_MAKEFILE=ON
         cmake --build . --parallel 2
@@ -80,13 +83,14 @@ 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_REGIONS=OFF -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -104,13 +108,14 @@ 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_REGIONS=OFF -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -132,14 +137,15 @@ jobs:
         sudo apt-get install clang-5.0 gfortran libopenmpi-dev python3
         sudo .github/workflows/dependencies/install_spack
     - name: Build
+      # Clang 5 does not handle GCC 10's STL in C++17-mode
       env: {CC: clang-5.0, CXX: clang++-5.0, CXXFLAGS: -Werror -Wno-deprecated-declarations, OPENPMD2_ADIOS2_SCHEMA: 20210209}
       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_REGIONS=OFF -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -164,7 +170,7 @@ 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_REGIONS=ON -DopenPMD_USE_INVASIVE_TESTS=ON -DCMAKE_VERBOSE_MAKEFILE=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -221,7 +227,7 @@ 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
 
@@ -242,7 +248,7 @@ 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
@@ -255,19 +261,21 @@ 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   \
           -DopenPMD_USE_ADIOS1=ON \
           -DopenPMD_USE_ADIOS2=ON \
+          -DopenPMD_USE_REGIONS=OFF \
           -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
@@ -286,7 +294,7 @@ 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_REGIONS=ON -DopenPMD_USE_INVASIVE_TESTS=ON
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -333,15 +341,20 @@ jobs:
         sudo .github/workflows/dependencies/install_icc
     - name: Build
       env: {CXXFLAGS: -Werror -Wno-deprecated-declarations}
+      # C++17 is advertised, but is 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           \
-          -DopenPMD_USE_MPI=OFF
+          -DopenPMD_USE_MPI=OFF              \
+          -DopenPMD_USE_REGIONS=OFF
         cmake --build . --parallel 2
         ctest --output-on-failure
 
@@ -359,6 +372,7 @@ 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           \

CMakeLists.txt

@@ -63,6 +63,7 @@ openpmd_option(HDF5           "HDF5 backend (.h5 files)"                  AUTO)
 openpmd_option(ADIOS1         "ADIOS1 backend (.bp files)"                AUTO)
 openpmd_option(ADIOS2         "ADIOS2 backend (.bp files)"                AUTO)
 openpmd_option(PYTHON         "Enable Python bindings"                    AUTO)
+openpmd_option(REGIONS        "Enable region algebra (requires C++17)"    AUTO)
 
 option(openPMD_INSTALL               "Add installation targets"             ON)
 option(openPMD_HAVE_PKGCONFIG        "Generate a .pc file for pkg-config"   ON)
@@ -363,6 +364,19 @@ else()
     set(openPMD_HAVE_PYTHON FALSE)
 endif()
 
+# Region algebra
+if(openPMD_USE_REGIONS STREQUAL AUTO)
+    # Enable regions by default only when building with at least C++17
+    if ("cxx_std_17" IN_LIST CMAKE_CXX_COMPILE_FEATURES)
+        set(openPMD_HAVE_REGIONS TRUE)
+    else()
+        set(openPMD_HAVE_REGIONS FALSE)
+    endif()
+elseif(openPMD_USE_REGIONS)
+    set(openPMD_HAVE_REGIONS TRUE)
+else()
+    set(openPMD_HAVE_REGIONS FALSE)
+endif()
 
 # Targets #####################################################################
 #
@@ -723,6 +737,13 @@ set(openPMD_TEST_NAMES
     SerialIO
     ParallelIO
 )
+if(openPMD_HAVE_REGIONS)
+    list(APPEND openPMD_TEST_NAMES
+        Box
+        Point
+        Region
+    )
+endif()
 # command line tools
 set(openPMD_CLI_TOOL_NAMES
     ls
@@ -749,6 +770,11 @@ set(openPMD_EXAMPLE_NAMES
     10_streaming_read
     12_span_write
 )
+if(openPMD_HAVE_REGIONS)
+    list(APPEND openPMD_EXAMPLE_NAMES
+        13_regions
+    )
+endif()
 set(openPMD_PYTHON_EXAMPLE_NAMES
     2_read_serial
     2a_read_thetaMode_serial
@@ -804,6 +830,13 @@ if(openPMD_BUILD_TESTING)
         else()
             target_link_libraries(${testname}Tests PRIVATE CatchMain)
         endif()
+        if(${testname} MATCHES "(Point)|(Box)|(Region)")
+            target_compile_features(${testname}Tests PUBLIC cxx_std_17)
+            set_target_properties(${testname}Tests PROPERTIES
+                CXX_EXTENSIONS OFF
+                CXX_STANDARD_REQUIRED ON
+            )
+        endif()
     endforeach()
 endif()
 
@@ -824,6 +857,13 @@ if(openPMD_BUILD_EXAMPLES)
         else()
             add_executable(${examplename} examples/${examplename}.cpp)
             target_link_libraries(${examplename} PRIVATE openPMD)
+            if(${examplename} MATCHES "13_.+$")
+                target_compile_features(${examplename} PUBLIC cxx_std_17)
+                set_target_properties(${examplename} PROPERTIES
+                    CXX_EXTENSIONS OFF
+                    CXX_STANDARD_REQUIRED ON
+                )
+            endif()
         endif()
     endforeach()
 endif()