added direct hdf5 call for heatTransfer test

examples/heatTransfer/write/IO_ph5.cpp

+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * IO_ADIOS2.cpp
+ *
+ *  Created on: Feb 2017
+ *      Author: Norbert Podhorszki
+ */
+
+#include "IO.h"
+
+#include <string>
+#include <stdexcept>
+#include <hdf5.h>
+#include <memory>
+#include <ios>
+#include <iostream>
+
+class HDF5NativeWriter
+{
+
+public:
+  HDF5NativeWriter(const std::string& fileName);
+  ~HDF5NativeWriter();
+
+  bool Advance();
+  void Close();
+  void CheckWriteGroup();
+
+  void WriteScalar(const std::string& varName, const void *data, hid_t h5Type);
+  void WriteSimple(const std::string& varName, int dimSize, const void *data, hid_t h5Type,  const hsize_t* shape, const hsize_t* offset, const hsize_t* count);
+
+  int m_CurrentTimeStep;
+  unsigned int m_TotalTimeSteps;
+
+private:
+  hid_t m_FilePropertyListId;
+  hid_t m_FileId;
+  hid_t m_GroupId;
+};
+
+HDF5NativeWriter::HDF5NativeWriter(const std::string& fileName)
+  : m_CurrentTimeStep(0), m_TotalTimeSteps(0)
+{
+  m_FilePropertyListId = H5Pcreate(H5P_FILE_ACCESS);
+
+#ifdef ADIOS2_HAVE_MPI
+  // read a file collectively
+  H5Pset_fapl_mpio(m_FilePropertyListId, MPI_COMM_WORLD, MPI_INFO_NULL);
+#endif
+
+  m_FileId = H5Fcreate(fileName.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT,
+		       m_FilePropertyListId);
+
+  if (m_FileId < 0)
+    {
+      throw std::runtime_error("Unable to open " + fileName + " for reading");
+    }
+
+  std::string ts0 = "/TimeStep0";
+
+  m_GroupId = H5Gcreate2(m_FileId, ts0.c_str(), H5P_DEFAULT,
+			 H5P_DEFAULT, H5P_DEFAULT);
+  if (m_GroupId < 0)
+    {
+      throw std::runtime_error("HDF5: Unable to create group " + ts0);
+    }
+}
+
+HDF5NativeWriter::~HDF5NativeWriter()
+{
+  Close();
+}
+
+void HDF5NativeWriter::Close()
+{
+  if (m_FileId < 0)
+    return;
+
+  hid_t s = H5Screate(H5S_SCALAR);
+  hid_t attr = H5Acreate(m_FileId, "NumTimeSteps", H5T_NATIVE_UINT, s,
+			 H5P_DEFAULT, H5P_DEFAULT);
+  uint totalTimeSteps = m_CurrentTimeStep + 1;
+
+  if (m_GroupId < 0)
+    {
+      totalTimeSteps = m_CurrentTimeStep;
+    }  
+  H5Awrite(attr, H5T_NATIVE_UINT, &totalTimeSteps);
+  H5Sclose(s);
+  H5Aclose(attr);
+
+
+  if (m_GroupId >= 0) 
+    {
+      H5Gclose(m_GroupId);
+      m_GroupId = -1;
+    } 
+
+  H5Fclose(m_FileId);
+  m_FileId = -1;
+  H5Pclose(m_FilePropertyListId);
+}
+
+bool HDF5NativeWriter::Advance()
+{
+  if (m_GroupId >= 0)
+    {
+      H5Gclose(m_GroupId);
+      m_GroupId = -1;
+    }
+
+  ++m_CurrentTimeStep;
+
+  return true;
+}
+
+
+void HDF5NativeWriter::CheckWriteGroup()
+{
+  if (m_GroupId >= 0)
+    {
+      return;
+    }
+
+  std::string timeStepName = "/TimeStep" + std::to_string(m_CurrentTimeStep);
+  m_GroupId = H5Gcreate2(m_FileId, timeStepName.c_str(), H5P_DEFAULT,
+			 H5P_DEFAULT, H5P_DEFAULT);
+  if (m_GroupId < 0)
+    {
+      throw std::runtime_error("HDF5: Unable to create group " +
+			       timeStepName);
+    }
+}
+
+
+void HDF5NativeWriter::WriteScalar(const std::string& varName, const void *data, hid_t h5Type)
+{
+  CheckWriteGroup();
+  // scalar
+  hid_t filespaceID = H5Screate(H5S_SCALAR);
+  hid_t dsetID =
+    H5Dcreate(m_GroupId, varName.c_str(), h5Type,
+	      filespaceID, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  herr_t status =
+    H5Dwrite(dsetID, h5Type, H5S_ALL, H5S_ALL, H5P_DEFAULT, data);
+  
+  H5Sclose(filespaceID);
+  H5Dclose(dsetID);
+
+}
+
+void HDF5NativeWriter::WriteSimple(const std::string& varName, int dimSize, const void *data, hid_t h5Type,  const hsize_t* shape, const hsize_t* offset, const hsize_t* count)
+{  
+  CheckWriteGroup();
+  hid_t fileSpace = H5Screate_simple(dimSize, shape, NULL);
+
+  hid_t dsetID =
+    H5Dcreate(m_GroupId, varName.c_str(), h5Type,
+	      fileSpace, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  
+  hid_t memSpace = H5Screate_simple(dimSize, count, NULL);
+  
+  // Select hyperslab
+  fileSpace = H5Dget_space(dsetID);
+  H5Sselect_hyperslab(fileSpace, H5S_SELECT_SET, offset, NULL,
+		      count, NULL);
+
+  //  Create property list for collective dataset write.
+  
+  hid_t plistID = H5Pcreate(H5P_DATASET_XFER);
+#ifdef ADIOS2_HAVE_MPI
+  H5Pset_dxpl_mpio(plistID, H5FD_MPIO_COLLECTIVE);
+#endif
+  herr_t status;
+  
+  status = H5Dwrite(dsetID, h5Type, memSpace, fileSpace, plistID, data);
+  
+  if (status < 0)
+    {
+      // error
+      std::cerr << " Write failed. " << std::endl;
+    }
+  
+  H5Dclose(dsetID);
+  H5Sclose(fileSpace);
+  H5Sclose(memSpace);
+  H5Pclose(plistID); 
+}
+
+//
+//
+std::shared_ptr<HDF5NativeWriter> h5writer;
+//HDF5NativeWriter* h5writer;
+
+
+IO::IO(const Settings &s, MPI_Comm comm)
+{
+    m_outputfilename = s.outputfile + ".h5";
+
+    h5writer = std::make_shared<HDF5NativeWriter>(m_outputfilename);
+
+    if (h5writer == nullptr)
+        throw std::ios_base::failure("ERROR: failed to open ADIOS h5writer\n");
+}
+
+IO::~IO()
+{
+    h5writer->Close();
+    //delete h5writer;
+}
+
+void IO::write(int step, const HeatTransfer &ht, const Settings &s,
+               MPI_Comm comm)
+{
+    std::vector<hsize_t> dims   = {s.gndx, s.gndy};
+    std::vector<hsize_t> offset = {s.offsx, s.offsy};
+    std::vector<hsize_t> count  = {s.ndx, s.ndy};
+
+    h5writer->WriteSimple("T", 2, ht.data_noghost().data(), H5T_NATIVE_DOUBLE, dims.data(), offset.data(), count.data());
+    h5writer->WriteScalar("gndy", &(s.gndy), H5T_NATIVE_UINT);
+
+    h5writer->Advance();
+}