Merge pull request #1948 from bradking/parallel-adios-serial-hdf5

Allow building ADIOS with MPI using a serial HDF5
ornladios · Feb 13, 2020 · f391aa9 · f391aa9
2 parents 4cd6d90 + 5b2262d
commit f391aa9
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Showing 16 changed files with 115 additions and 113 deletions.
diff --git a/cmake/DetectOptions.cmake b/cmake/DetectOptions.cmake
@@ -155,21 +155,13 @@ endif()
 # HDF5
 if(ADIOS2_USE_HDF5 STREQUAL AUTO)
   find_package(HDF5 COMPONENTS C)
-  if(HDF5_FOUND AND
-     ((ADIOS2_HAVE_MPI AND HDF5_IS_PARALLEL) OR
-      (NOT ADIOS2_HAVE_MPI AND NOT HDF5_IS_PARALLEL)))
+  if(HDF5_FOUND AND (NOT HDF5_IS_PARALLEL OR ADIOS2_HAVE_MPI))
     set(ADIOS2_HAVE_HDF5 TRUE)
   endif()
 elseif(ADIOS2_USE_HDF5)
   find_package(HDF5 REQUIRED COMPONENTS C)
-  if(ADIOS2_HAVE_MPI)
-    if(NOT HDF5_IS_PARALLEL)
-      message(FATAL_ERROR "MPI is enabled but serial HDF5 is detected.")
-    endif()
-  else()
-    if(HDF5_IS_PARALLEL)
-      message(FATAL_ERROR "MPI is disabled but parallel HDF5 is detected.")
-    endif()
+  if(HDF5_IS_PARALLEL AND NOT ADIOS2_HAVE_MPI)
+    message(FATAL_ERROR "MPI is disabled but parallel HDF5 is detected.")
   endif()
   set(ADIOS2_HAVE_HDF5 TRUE)
 endif()

diff --git a/examples/heatTransfer/write/CMakeLists.txt b/examples/heatTransfer/write/CMakeLists.txt
@@ -37,18 +37,20 @@ if(ADIOS2_HAVE_HDF5)
     ${HDF5_C_LIBRARIES} MPI::MPI_C ${CMAKE_THREAD_LIBS_INIT}
   )
 
-  add_executable(heatTransfer_write_ph5
-    main.cpp
-    HeatTransfer.cpp
-    Settings.cpp
-    IO_ph5.cpp
-  )
-  target_include_directories(heatTransfer_write_ph5
-    PRIVATE ${HDF5_C_INCLUDE_DIRS}
-  )
-  target_link_libraries(heatTransfer_write_ph5
-    ${HDF5_C_LIBRARIES} MPI::MPI_C ${CMAKE_THREAD_LIBS_INIT}
-  )
+  if(HDF5_IS_PARALLEL)
+    add_executable(heatTransfer_write_ph5
+      main.cpp
+      HeatTransfer.cpp
+      Settings.cpp
+      IO_ph5.cpp
+    )
+    target_include_directories(heatTransfer_write_ph5
+      PRIVATE ${HDF5_C_INCLUDE_DIRS}
+    )
+    target_link_libraries(heatTransfer_write_ph5
+      ${HDF5_C_LIBRARIES} MPI::MPI_C ${CMAKE_THREAD_LIBS_INIT}
+    )
+  endif()
 
   if(NOT (HDF5_VERSION VERSION_LESS 1.11))
     add_executable(heatTransfer_write_h5mixer

diff --git a/source/utils/adios_iotest/CMakeLists.txt b/source/utils/adios_iotest/CMakeLists.txt
@@ -13,7 +13,8 @@ if(WIN32)
   target_link_libraries(adios_iotest getopt)
 endif()
 
-if(ADIOS2_HAVE_HDF5)
+if(ADIOS2_HAVE_HDF5 AND HDF5_IS_PARALLEL)
+  target_compile_definitions(adios_iotest PRIVATE ADIOS2_HAVE_HDF5_PARALLEL)
   if(HDF5_C_INCLUDE_DIRS)
     target_include_directories(adios_iotest PRIVATE ${HDF5_C_INCLUDE_DIRS})
   else()

diff --git a/source/utils/adios_iotest/ioGroup.cpp b/source/utils/adios_iotest/ioGroup.cpp
@@ -7,7 +7,7 @@
 #include "ioGroup.h"
 #include "adios2/common/ADIOSConfig.h"
 
-#ifdef ADIOS2_HAVE_HDF5
+#ifdef ADIOS2_HAVE_HDF5_PARALLEL
 #include "hdf5.h"
 #endif
 
@@ -20,7 +20,7 @@ std::shared_ptr<ioGroup> createGroup(const std::string &name, IOLib iolib,
     case IOLib::ADIOS:
         gp = std::make_shared<adiosIOGroup>(name, adiosobj);
         break;
-#ifdef ADIOS2_HAVE_HDF5
+#ifdef ADIOS2_HAVE_HDF5_PARALLEL
     case IOLib::HDF5:
         gp = std::make_shared<hdf5IOGroup>(name);
         break;

diff --git a/source/utils/adios_iotest/settings.cpp b/source/utils/adios_iotest/settings.cpp
@@ -24,7 +24,7 @@ struct option options[] = {{"help", no_argument, NULL, 'h'},
                            {"strong-scaling", no_argument, NULL, 's'},
                            {"weak-scaling", no_argument, NULL, 'w'},
                            {"timer", no_argument, NULL, 't'},
-#ifdef ADIOS2_HAVE_HDF5
+#ifdef ADIOS2_HAVE_HDF5_PARALLEL
                            {"hdf5", no_argument, NULL, 'H'},
 #endif
                            {NULL, 0, NULL, 0}};
@@ -53,7 +53,7 @@ void Settings::displayHelp()
         << "  -s OR -w:  strong or weak scaling. \n"
         << "             Dimensions in config are treated accordingly\n"
         << "  -x file    ADIOS configuration XML file\n"
-#ifdef ADIOS2_HAVE_HDF5
+#ifdef ADIOS2_HAVE_HDF5_PARALLEL
         << "  --hdf5     Use native Parallel HDF5 instead of ADIOS for I/O\n"
 #endif
         << "  -v         increase verbosity\n"
@@ -105,7 +105,7 @@ int Settings::processArgs(int argc, char *argv[])
                 displayHelp();
             }
             return 1;
-#ifdef ADIOS2_HAVE_HDF5
+#ifdef ADIOS2_HAVE_HDF5_PARALLEL
         case 'H':
             iolib = IOLib::HDF5;
             break;

diff --git a/source/utils/adios_iotest/settings.h b/source/utils/adios_iotest/settings.h
@@ -22,7 +22,7 @@
 enum class IOLib
 {
     ADIOS
-#ifdef ADIOS2_HAVE_HDF5
+#ifdef ADIOS2_HAVE_HDF5_PARALLEL
     ,
     HDF5
 #endif

diff --git a/source/utils/adios_iotest/stream.cpp b/source/utils/adios_iotest/stream.cpp
@@ -10,7 +10,7 @@
 #include "adiosStream.h"
 #include "stream.h"
 
-#ifdef ADIOS2_HAVE_HDF5
+#ifdef ADIOS2_HAVE_HDF5_PARALLEL
 #include "hdf5Stream.h"
 #endif
 
@@ -65,7 +65,7 @@ std::shared_ptr<Stream> openStream(const std::string &streamName,
         sp = std::make_shared<adiosStream>(s);
         break;
     }
-#ifdef ADIOS2_HAVE_HDF5
+#ifdef ADIOS2_HAVE_HDF5_PARALLEL
     case IOLib::HDF5:
     {
         auto s = hdf5Stream(streamName, mode, comm);

diff --git a/testing/adios2/engine/common/CMakeLists.txt b/testing/adios2/engine/common/CMakeLists.txt
@@ -20,7 +20,7 @@ gtest_add_tests_helper(Common ${test_mpi} "" Engine. .File
   EXTRA_ARGS "File" "1"
 )
 
-if(ADIOS2_HAVE_HDF5)
+if(ADIOS2_HAVE_HDF5 AND HDF5_IS_PARALLEL)
   gtest_add_tests_helper(Common ${test_mpi} "" Engine. .HDF5
     EXTRA_ARGS "HDF5" "1"
   )

diff --git a/testing/adios2/engine/hdf5/CMakeLists.txt b/testing/adios2/engine/hdf5/CMakeLists.txt
@@ -3,18 +3,25 @@
 # accompanying file Copyright.txt for details.
 #------------------------------------------------------------------------------#
 
-gtest_add_tests_helper(WriteReadAsStream ${test_mpi} HDF5 Engine.HDF5. "")
-gtest_add_tests_helper(StreamWriteReadHighLevelAPI ${test_mpi}
+if(ADIOS2_HAVE_MPI AND HDF5_IS_PARALLEL)
+  set(hdf5_mpi TRUE)
+  add_definitions(-DTEST_HDF5_MPI)
+else()
+  set(hdf5_mpi FALSE)
+endif()
+
+gtest_add_tests_helper(WriteReadAsStream ${hdf5_mpi} HDF5 Engine.HDF5. "")
+gtest_add_tests_helper(StreamWriteReadHighLevelAPI ${hdf5_mpi}
   HDF5 Engine.HDF5. ""
 )
-gtest_add_tests_helper(WriteReadAttributesADIOS2 ${test_mpi}
+gtest_add_tests_helper(WriteReadAttributesADIOS2 ${hdf5_mpi}
   HDF5 Engine.HDF5. ""
 )
-gtest_add_tests_helper(WriteMemorySelectionRead  ${test_mpi}
+gtest_add_tests_helper(WriteMemorySelectionRead  ${hdf5_mpi}
   HDF5 Engine.HDF5. ""
 )
 
-gtest_add_tests_helper(NativeHDF5WriteRead ${test_mpi} "" Engine.HDF5. "")
+gtest_add_tests_helper(NativeHDF5WriteRead ${hdf5_mpi} "" Engine.HDF5. "")
 if(HDF5_C_INCLUDE_DIRS)
   target_include_directories(Test.Engine.HDF5.NativeHDF5WriteRead
     PRIVATE ${HDF5_C_INCLUDE_DIRS}

diff --git a/testing/adios2/engine/hdf5/TestHDF5StreamWriteReadHighLevelAPI.cpp b/testing/adios2/engine/hdf5/TestHDF5StreamWriteReadHighLevelAPI.cpp
@@ -39,14 +39,14 @@ TEST_F(StreamWriteReadHighLevelAPI_HDF5, ADIOS2H5writeRead1D8)
     // Number of steps
     const size_t NSteps = 3;
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
     MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
 #endif
 
     // write test data using H5
     {
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
         adios2::fstream oStream(fname, adios2::fstream::out, MPI_COMM_WORLD,
                                 "HDF5");
 #else
@@ -101,7 +101,7 @@ TEST_F(StreamWriteReadHighLevelAPI_HDF5, ADIOS2H5writeRead1D8)
         adios2::fstream iStream;
         EXPECT_FALSE(iStream);
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
         iStream.open(fname, adios2::fstream::in, MPI_COMM_WORLD, "HDF5");
 #else
         iStream.open(fname, adios2::fstream::in, "HDF5");
@@ -272,14 +272,14 @@ TEST_F(StreamWriteReadHighLevelAPI_HDF5, ADIOS2H5writeRead2D2x4)
     // Number of steps
     const std::size_t NSteps = 3;
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
     MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
 #endif
 
     // write test data using ADIOS2
     {
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
         adios2::fstream oStream(fname, adios2::fstream::out, MPI_COMM_WORLD,
                                 "HDF5");
 #else
@@ -316,7 +316,7 @@ TEST_F(StreamWriteReadHighLevelAPI_HDF5, ADIOS2H5writeRead2D2x4)
 
     // READ
     {
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
         adios2::fstream iStream(fname, adios2::fstream::in, MPI_COMM_WORLD,
                                 "HDF5");
 #else
@@ -391,14 +391,14 @@ TEST_F(StreamWriteReadHighLevelAPI_HDF5, ADIOS2H5writeRead2D4x2)
     // Number of steps
     const std::size_t NSteps = 3;
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
     MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
 #endif
 
     // write test data using ADIOS2
     {
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
         adios2::fstream oStream(fname, adios2::fstream::out, MPI_COMM_WORLD,
                                 "HDF5");
 #else
@@ -437,7 +437,7 @@ TEST_F(StreamWriteReadHighLevelAPI_HDF5, ADIOS2H5writeRead2D4x2)
     }
 
     {
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
         adios2::fstream iStream(fname, adios2::fstream::in, MPI_COMM_WORLD,
                                 "HDF5");
 #else
@@ -501,7 +501,7 @@ TEST_F(StreamWriteReadHighLevelAPI_HDF5, DoubleOpenException)
     const std::string fname("ADIOS2H5_hl_exception.h5");
 
     {
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
         adios2::fstream oStream(fname, adios2::fstream::out, MPI_COMM_WORLD,
                                 "HDF5");
         EXPECT_THROW(oStream.open("second", adios2::fstream::out,
@@ -519,15 +519,15 @@ TEST_F(StreamWriteReadHighLevelAPI_HDF5, DoubleOpenException)
 
 int main(int argc, char **argv)
 {
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Init(nullptr, nullptr);
 #endif
 
     int result;
     ::testing::InitGoogleTest(&argc, argv);
     result = RUN_ALL_TESTS();
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Finalize();
 #endif
 

diff --git a/testing/adios2/engine/hdf5/TestHDF5WriteMemorySelectionRead.cpp b/testing/adios2/engine/hdf5/TestHDF5WriteMemorySelectionRead.cpp
@@ -249,12 +249,12 @@ void HDF5Steps1D(const size_t ghostCells)
     // Number of steps
     const size_t NSteps = 3;
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
     MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
 #endif
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     adios2::ADIOS adios(MPI_COMM_WORLD, adios2::DebugON);
 #else
     adios2::ADIOS adios(true);
@@ -331,7 +331,7 @@ void HDF5Steps1D(const size_t ghostCells)
         }
         h5Writer.Close();
     }
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Barrier(MPI_COMM_WORLD);
 #endif
     // Reader
@@ -485,12 +485,12 @@ void HDF5Steps2D4x2(const size_t ghostCells)
     // Number of steps
     const size_t NSteps = 3;
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
     MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
 #endif
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     adios2::ADIOS adios(MPI_COMM_WORLD, adios2::DebugON);
 #else
     adios2::ADIOS adios(true);
@@ -567,7 +567,7 @@ void HDF5Steps2D4x2(const size_t ghostCells)
         }
         h5Writer.Close();
     }
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Barrier(MPI_COMM_WORLD);
 #endif
     // Reader
@@ -733,12 +733,12 @@ void HDF5Steps3D8x2x4(const size_t ghostCells)
     // Number of steps
     const size_t NSteps = 3;
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Comm_rank(MPI_COMM_WORLD, &mpiRank);
     MPI_Comm_size(MPI_COMM_WORLD, &mpiSize);
 #endif
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     adios2::ADIOS adios(MPI_COMM_WORLD, adios2::DebugON);
 #else
     adios2::ADIOS adios(true);
@@ -825,7 +825,7 @@ void HDF5Steps3D8x2x4(const size_t ghostCells)
         }
         h5Writer.Close();
     }
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Barrier(MPI_COMM_WORLD);
 #endif
     // Reader
@@ -1042,7 +1042,7 @@ INSTANTIATE_TEST_CASE_P(ghostCells, HDF5WriteMemSelReadVector,
 
 int main(int argc, char **argv)
 {
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Init(nullptr, nullptr);
 #endif
 
@@ -1058,7 +1058,7 @@ int main(int argc, char **argv)
 
     result = RUN_ALL_TESTS();
 
-#ifdef ADIOS2_HAVE_MPI
+#ifdef TEST_HDF5_MPI
     MPI_Finalize();
 #endif