Feature/hdf5 output

Code/CMakeLists.txt

@@ -5,7 +5,8 @@
 cmake_minimum_required (VERSION 3.13)
 
 project(HemeLB)
-
+option(USE_HDF5 "Enable HDF5 support" ON)
+message(STATUS "USE_HDF5 = ${USE_HDF5}")
 set(HEMELB_ROOT_DIR ${CMAKE_CURRENT_SOURCE_DIR}/..)
 
 list(INSERT CMAKE_MODULE_PATH 0 "${HEMELB_ROOT_DIR}/CMake")
@@ -84,10 +85,18 @@ find_hemelb_dependency(ZLIB REQUIRED)
 link_libraries(MPI::MPI_CXX)
 link_libraries(Boost::headers)
 
-if(HEMELB_BUILD_RBC)
-  # Work around some installs of HDF5 having proper targets and others
-  # not...
+# if(HEMELB_BUILD_RBC)
+#   # Work around some installs of HDF5 having proper targets and others
+#   # not...
+#   include(UseHDF5)
+#   find_hemelb_dependency(VTK REQUIRED)
+# endif()
+if(USE_HDF5)
   include(UseHDF5)
+  add_definitions(-DUSE_HDF5)
+endif()
+
+if(HEMELB_BUILD_RBC)
   find_hemelb_dependency(VTK REQUIRED)
 endif()
 

Code/configuration/SimConfig.cc

@@ -358,7 +358,11 @@ namespace hemelb::configuration
       }
 
       propertyoutputEl.GetAttributeOrThrow("period", file.frequency);
-
+      // attend to find property "format", if exists, read it
+      // otherwise default to "xdr"
+      file.format = propertyoutputEl.GetAttributeMaybe("format").value_or("xdr");
+
+
       io::xml::Element geometryEl = propertyoutputEl.GetChildOrThrow("geometry");
       auto type = geometryEl.GetAttributeOrThrow("type");
 

Code/configuration/SimConfig.h

@@ -155,11 +155,11 @@ namespace hemelb::configuration
     };
 
     struct IoletConfigBase {
-        PhysicalPosition position;
-        util::Vector3D<double> normal;
-        std::optional<std::uint64_t> warmup_steps;
-        std::optional<FlowExtensionConfig> flow_extension;
-        std::vector<CellInserterConfig> cell_inserters;
+        PhysicalPosition position{}; // make sure position is initialized to zero
+        util::Vector3D<double> normal{}; 
+        std::optional<std::uint64_t> warmup_steps = std::nullopt; // initialized to no warmup steps
+        std::optional<FlowExtensionConfig> flow_extension = std::nullopt; // initialized to no flow extension
+        std::vector<CellInserterConfig> cell_inserters; 
     };
 
     // Consider removing

Code/extraction/CMakeLists.txt

@@ -3,9 +3,52 @@
 # file AUTHORS. This software is provided under the terms of the
 # license in the file LICENSE.
 
-add_library(hemelb_extraction OBJECT
+
+set(EXTRACTION_SOURCES
   GeometrySelector.cc
-  StraightLineGeometrySelector.cc LocalPropertyOutput.cc
-  IterableDataSource.cc PlaneGeometrySelector.cc PropertyActor.cc
-  PropertyWriter.cc WholeGeometrySelector.cc LbDataSourceIterator.cc
-  GeometrySurfaceSelector.cc SurfacePointSelector.cc LocalDistributionInput.cc)
+  StraightLineGeometrySelector.cc
+  IterableDataSource.cc
+  PlaneGeometrySelector.cc
+  PropertyActor.cc
+  PropertyWriter.cc
+  WholeGeometrySelector.cc
+  LbDataSourceIterator.cc
+  GeometrySurfaceSelector.cc
+  SurfacePointSelector.cc
+  LocalDistributionInput.cc
+
+  # reconstructed base class from the original class
+  LocalPropertyOutput.cc
+  # subclass for original XDR functionality
+  XdrPropertyOutput.cc
+  )
+
+# new source files for HDF5 support
+# only include these if USE_HDF5 is enabled
+if(USE_HDF5)
+  list(APPEND EXTRACTION_SOURCES
+    LocalPropertyHdf5Output.cc
+  )
+endif()
+
+# use the list of sources to create the hemelb_extraction library
+add_library(hemelb_extraction OBJECT
+  ${EXTRACTION_SOURCES}
+)
+
+# new CMake module for HDF5 support
+# only include this if USE_HDF5 is enabled
+if(USE_HDF5)
+  # include the HDF5 module into hemelb_extraction module's list of dependencies
+  # PUBLIC makes the include directories and libraries available to consumers of hemelb_extraction
+  target_include_directories(hemelb_extraction PUBLIC
+    ${HDF5_INCLUDE_DIRS}
+  )
+
+  # link the hemelb_extraction library with HDF5
+  target_link_libraries(hemelb_extraction PUBLIC
+    HDF5::HDF5
+  )
+  # define a preprocessor macro to indicate that HDF5 is being used
+  target_compile_definitions(hemelb_extraction PUBLIC USE_HDF5)
+endif()

Code/extraction/LoacalPropertyHdf5Output.cc

@@ -0,0 +1,79 @@
+// LocalPropertyHdf5Output.cc
+#include "LocalPropertyHdf5Output.h"
+#ifdef USE_HDF5
+#include <vector>
+#include <cassert>
+
+namespace hemelb::io {
+
+#pragma pack(push,1)
+struct PointRec
+{
+  uint32_t x, y, z;
+  double   pressure;
+};
+#pragma pack(pop)
+
+LocalPropertyHdf5Output::LocalPropertyHdf5Output(IterableDataSource& src,
+                                                 const PropertyOutputFile& spec,
+                                                 const net::IOCommunicator& comms)
+  : LocalPropertyOutputBase(src, spec, comms),
+    comm_(comms.GetCommunicator())
+{
+  // ---- 定义 compound datatype ----
+  memType_ = H5Tcreate(H5T_COMPOUND, sizeof(PointRec));
+  H5Tinsert(memType_, "x", HOFFSET(PointRec, x), H5T_NATIVE_UINT32);
+  H5Tinsert(memType_, "y", HOFFSET(PointRec, y), H5T_NATIVE_UINT32);
+  H5Tinsert(memType_, "z", HOFFSET(PointRec, z), H5T_NATIVE_UINT32);
+  H5Tinsert(memType_, "p", HOFFSET(PointRec, pressure), H5T_NATIVE_DOUBLE);
+}
+
+void LocalPropertyHdf5Output::StartFile(const std::string& fn)
+{
+  hid_t fapl = H5Pcreate(H5P_FILE_ACCESS);
+  H5Pset_fapl_mpio(fapl, comm_, MPI_INFO_NULL);
+  file_ = H5Fcreate(fn.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, fapl);
+  H5Pclose(fapl);
+
+  const hsize_t global = globalSiteCount;      // 这个成员继承自基类
+  fileSpace_ = H5Screate_simple(1, &global, nullptr);
+  dset_      = H5Dcreate(file_, "points", memType_, fileSpace_,
+                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+}
+
+void LocalPropertyHdf5Output::Write(unsigned long /*ts*/, unsigned long /*total*/)
+{
+  std::vector<PointRec> buf;
+  buf.reserve(localSiteCount);
+
+  while (dataSource.ReadNext()) {
+    const auto& pos = dataSource.GetPosition();
+    buf.push_back({pos.x, pos.y, pos.z, dataSource.GetPressure()});
+  }
+  assert(buf.size() == localSiteCount);
+
+  // 选择 hyperslab
+  const hsize_t start = localSiteStartRow;
+  const hsize_t count = localSiteCount;
+  H5Sselect_hyperslab(fileSpace_, H5S_SELECT_SET, &start, nullptr, &count, nullptr);
+
+  hid_t memSpace = H5Screate_simple(1, &count, nullptr);
+  hid_t xfer     = H5Pcreate(H5P_DATASET_XFER);
+  H5Pset_dxpl_mpio(xfer, H5FD_MPIO_COLLECTIVE);
+
+  H5Dwrite(dset_, memType_, memSpace, fileSpace_, xfer, buf.data());
+
+  H5Sclose(memSpace);
+  H5Pclose(xfer);
+}
+
+void LocalPropertyHdf5Output::Close()
+{
+  if (dset_      >= 0) H5Dclose(dset_);
+  if (fileSpace_ >= 0) H5Sclose(fileSpace_);
+  if (memType_   >= 0) H5Tclose(memType_);
+  if (file_      >= 0) H5Fclose(file_);
+}
+
+} // namespace hemelb::io
+#endif // USE_HDF5