ADIOS1: Fix Serial Builds, CI: Clang 10->12

.github/ci/spack-envs/clang10_nopy_ompi_h5_ad1_ad2/spack.yaml → .github/ci/spack-envs/clang12_py38_nompi_h5_ad1_ad2/spack.yaml

@@ -9,25 +9,19 @@ spack:
   - adios
   - adios2
   - hdf5
-  - openmpi
 
   packages:
     hdf5:
       variants: ~mpi
     adios:
-      variants: ~zfp ~sz ~lz4 ~blosc
+      variants: ~mpi ~zfp ~sz ~lz4 ~blosc
     adios2:
-      variants: ~zfp ~sz ~png ~dataman ~python ~fortran ~ssc ~shared ~bzip2
+      variants: ~mpi ~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"
@@ -43,7 +37,7 @@ spack:
       variants: ~fortran
       providers:
         mpi: [openmpi]
-      compiler: [clang@10.0.0]
+      compiler: [clang@12.0.0]
 
   compilers:
   - compiler:
@@ -53,11 +47,11 @@ spack:
       modules: []
       operating_system: ubuntu20.04
       paths:
-        cc: /usr/lib/llvm-10/bin/clang
-        cxx: /usr/lib/llvm-10/bin/clang++
+        cc: /usr/lib/llvm-12/bin/clang
+        cxx: /usr/lib/llvm-12/bin/clang++
         f77: /usr/bin/gfortran
         fc: /usr/bin/gfortran
-      spec: clang@10.0.0
+      spec: clang@12.0.0
       target: x86_64
 
   config:

.github/workflows/linux.yml

@@ -106,29 +106,33 @@ jobs:
 # TODO
 #  clang6_py36_nompi_h5_ad1_ad2_libcpp
 
-  clang10_py38_nompi_h5_ad1_ad2_libcpp:
+  clang12_py38_nompi_h5_ad1_ad2:
     runs-on: ubuntu-20.04
     if: github.event.pull_request.draft == false
     steps:
     - uses: actions/checkout@v2
+    - name: Spack Cache
+      uses: actions/cache@v2
+      with: {path: /opt/spack, key: clang12_py38_nompi_h5_ad1_ad2 }
     - name: Install
       run: |
         sudo apt-get update
-        sudo apt-get install clang-10 libc++-dev libc++abi-dev libhdf5-dev python3
-        python3 -m pip install -U pip
-        python3 -m pip install -U numpy
-#       TODO ADIOS1 ADIOS2
+        sudo apt-get install clang-12 libhdf5-dev python3 python3-pip python3-numpy python3-pandas
+        sudo .github/workflows/dependencies/install_spack
     - name: Build
-      env: {CC: clang-10, CXX: clang++-10, CXXFLAGS: -Werror -Wno-deprecated-declarations}
-      # TODO
-      # , CXXFLAGS: -nostdinc++ -I/usr/include/c++/10 -I/usr/include/x86_64-linux-gnu/c++/10/, LDFLAGS: -stdlib=libc++ -lc++ -lc++abi}
+      env: {CC: clang-12, CXX: clang++-12, CXXFLAGS: -Werror -Wno-deprecated-declarations}
       run: |
+        eval $(spack env activate --sh .github/ci/spack-envs/clang12_py38_nompi_h5_ad1_ad2/)
+        spack install
+
         share/openPMD/download_samples.sh build
         chmod u-w build/samples/git-sample/*.h5
         cmake -S . -B build \
           -DopenPMD_USE_PYTHON=ON \
           -DopenPMD_USE_MPI=OFF   \
           -DopenPMD_USE_HDF5=ON   \
+          -DopenPMD_USE_ADIOS1=ON \
+          -DopenPMD_USE_ADIOS2=ON \
           -DopenPMD_USE_INVASIVE_TESTS=ON \
           -DCMAKE_VERBOSE_MAKEFILE=ON
         cmake --build build --parallel 2

CMakeLists.txt

@@ -574,13 +574,6 @@ if(openPMD_HAVE_ADIOS1)
     target_include_directories(openPMD.ADIOS1.Parallel PRIVATE
         ${openPMD_SOURCE_DIR}/include ${openPMD_BINARY_DIR}/include)
 
-    if(openPMD_HAVE_MPI)
-        target_link_libraries(openPMD.ADIOS1.Parallel PUBLIC ${openPMD_MPI_TARGETS})
-        target_compile_definitions(openPMD.ADIOS1.Parallel PRIVATE openPMD_HAVE_MPI=1)
-    else()
-        target_compile_definitions(openPMD.ADIOS1.Parallel PRIVATE openPMD_HAVE_MPI=0)
-    endif()
-
     target_include_directories(openPMD.ADIOS1.Serial SYSTEM PRIVATE
         $<TARGET_PROPERTY:openPMD::thirdparty::nlohmann_json,INTERFACE_INCLUDE_DIRECTORIES>
         $<TARGET_PROPERTY:openPMD::thirdparty::toml11,INTERFACE_INCLUDE_DIRECTORIES>)
@@ -610,7 +603,7 @@ if(openPMD_HAVE_ADIOS1)
     target_compile_definitions(openPMD.ADIOS1.Serial PRIVATE "${ADIOS_DEFINITIONS_SEQUENTIAL}")
     target_compile_definitions(openPMD.ADIOS1.Serial PRIVATE openPMD_HAVE_ADIOS1=1)
     target_compile_definitions(openPMD.ADIOS1.Serial PRIVATE openPMD_HAVE_MPI=0)
-    target_compile_definitions(openPMD.ADIOS1.Serial PRIVATE _NOMPI=1)
+    target_compile_definitions(openPMD.ADIOS1.Serial PRIVATE _NOMPI)  # ADIOS header
 
     if(openPMD_HAVE_MPI)
         set_target_properties(openPMD.ADIOS1.Parallel PROPERTIES
@@ -631,10 +624,16 @@ if(openPMD_HAVE_ADIOS1)
         foreach(adlib ${ADIOS_LIBRARIES})
             target_link_libraries(openPMD.ADIOS1.Parallel PRIVATE ${adlib})
         endforeach()
+        target_link_libraries(openPMD.ADIOS1.Parallel PUBLIC ${openPMD_MPI_TARGETS})
 
         target_include_directories(openPMD.ADIOS1.Parallel SYSTEM PRIVATE ${ADIOS_INCLUDE_DIRS})
         target_compile_definitions(openPMD.ADIOS1.Parallel PRIVATE "${ADIOS_DEFINITIONS}")
         target_compile_definitions(openPMD.ADIOS1.Parallel PRIVATE openPMD_HAVE_ADIOS1=1)
+        target_compile_definitions(openPMD.ADIOS1.Parallel PRIVATE openPMD_HAVE_MPI=1)
+    else()
+        target_compile_definitions(openPMD.ADIOS1.Parallel PRIVATE openPMD_HAVE_ADIOS1=0)
+        target_compile_definitions(openPMD.ADIOS1.Parallel PRIVATE openPMD_HAVE_MPI=0)
+        target_compile_definitions(openPMD.ADIOS1.Parallel PRIVATE _NOMPI)  # ADIOS header
     endif()
 
     # Runtime parameter and API status checks ("asserts")

src/IO/ADIOS/CommonADIOS1IOHandler.cpp

@@ -1788,6 +1788,7 @@ void CommonADIOS1IOHandlerImpl< ChildClass >::initJson(
 template class CommonADIOS1IOHandlerImpl< ADIOS1IOHandlerImpl >;
 #if openPMD_HAVE_MPI
 template class CommonADIOS1IOHandlerImpl< ParallelADIOS1IOHandlerImpl >;
-#endif // opepnPMD_HAVE_MPI
+#endif // openPMD_HAVE_MPI
+
+} // namespace openPMD
 #endif // openPMD_HAVE_ADIOS1
-}

src/IO/ADIOS/ParallelADIOS1IOHandler.cpp

@@ -346,7 +346,7 @@ ParallelADIOS1IOHandlerImpl::initialize_group(std::string const &name)
     return group;
 }
 
-#else
+#else // openPMD_HAVE_ADIOS1 && openPMD_HAVE_MPI
 #   if openPMD_HAVE_MPI
 ParallelADIOS1IOHandler::ParallelADIOS1IOHandler(std::string path,
                                                  Access at,
@@ -364,7 +364,7 @@ ParallelADIOS1IOHandler::ParallelADIOS1IOHandler(std::string path,
 {
     throw std::runtime_error("openPMD-api built without parallel ADIOS1 support");
 }
-#   endif
+#   endif // openPMD_HAVE_MPI
 
 ParallelADIOS1IOHandler::~ParallelADIOS1IOHandler() = default;
 
@@ -374,9 +374,11 @@ ParallelADIOS1IOHandler::flush()
     return std::future< void >();
 }
 
+#if openPMD_HAVE_ADIOS1
 void
 ParallelADIOS1IOHandler::enqueue(IOTask const&)
 {
 }
-#endif
-} // openPMD
+#endif // openPMD_HAVE_ADIOS1
+#endif // openPMD_HAVE_ADIOS1 && openPMD_HAVE_MPI
+} // namespace openPMD