added to handle common hdf5 operations for both read/write

source/adios2/engine/hdf5/HDF5Common.cpp

+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * HDF5Common.cpp
+ *
+ *  Created on: April 20, 2017
+ *      Author: Junmin
+ */
+
+#include <iostream> //needs to go away, this is just for demo purposes
+
+#include "engine/hdf5/HDF5Common.h"
+
+namespace adios
+{
+
+#define H5_ERROR std::cout<<"[ADIOS H5 ERROR] "
+
+HDF5Common::HDF5Common()
+  :_writeMode(false),
+   _total_timestep(0),
+   _currentTimeStep(0)
+{
+    DefH5T_COMPLEX_FLOAT = H5Tcreate(H5T_COMPOUND, sizeof(std::complex<float>));
+    H5Tinsert(DefH5T_COMPLEX_FLOAT, "freal", 0, H5T_NATIVE_FLOAT);
+    H5Tinsert(DefH5T_COMPLEX_FLOAT, "fimg", H5Tget_size(H5T_NATIVE_FLOAT),
+              H5T_NATIVE_FLOAT);
+
+    DefH5T_COMPLEX_DOUBLE =
+        H5Tcreate(H5T_COMPOUND, sizeof(std::complex<double>));
+    H5Tinsert(DefH5T_COMPLEX_DOUBLE, "dreal", 0, H5T_NATIVE_DOUBLE);
+    H5Tinsert(DefH5T_COMPLEX_DOUBLE, "dimg", H5Tget_size(H5T_NATIVE_DOUBLE),
+              H5T_NATIVE_DOUBLE);
+
+    DefH5T_COMPLEX_LongDOUBLE =
+        H5Tcreate(H5T_COMPOUND, sizeof(std::complex<long double>));
+    H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble real", 0, H5T_NATIVE_LDOUBLE);
+    H5Tinsert(DefH5T_COMPLEX_LongDOUBLE, "ldouble img",
+              H5Tget_size(H5T_NATIVE_LDOUBLE), H5T_NATIVE_LDOUBLE);    
+}
+
+
+void  HDF5Common::H5_Init(const std::string name, MPI_Comm m_MPIComm, bool toWrite)
+{
+    _writeMode = toWrite;
+
+    //
+    _plist_id = H5Pcreate(H5P_FILE_ACCESS);
+    
+#ifdef ADIOS2_HAVE_MPI
+    H5Pset_fapl_mpio(_plist_id, m_MPIComm, MPI_INFO_NULL);
+#endif      
+
+    std::string ts0 = "/TimeStep0";
+
+    if (toWrite) {
+      /*
+       * Create a new file collectively and release property list identifier.
+       */
+      _file_id = H5Fcreate(name.c_str(), H5F_ACC_TRUNC, H5P_DEFAULT, _plist_id);
+      if (_file_id >= 0) 
+      {
+	_group_id =
+	  H5Gcreate2(_file_id, ts0.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+      }
+    } else {
+      // read a file collectively
+      _file_id = H5Fopen(name.c_str(), H5F_ACC_RDONLY, H5P_DEFAULT);
+      if (_file_id >= 0) 
+      {
+	_group_id = H5Gopen(_file_id, ts0.c_str(), H5P_DEFAULT);	
+      }
+    }
+
+    H5Pclose(_plist_id);
+}
+	
+HDF5Common::~HDF5Common() {}
+
+void HDF5Common::WriteTimeSteps()
+{
+  if (_file_id < 0) 
+  {
+    //std::cerr<<"[ADIOS HDF5Error]: Invalid file to record timestep to."<<std::endl;
+    H5_ERROR<<"Invalid file to record timestep to."<<std::endl;
+    return;
+  }
+
+  hid_t s = H5Screate(H5S_SCALAR);
+
+  hid_t attr = H5Acreate(_file_id, "NumTimeSteps", H5T_NATIVE_UINT, s, H5P_DEFAULT, H5P_DEFAULT);
+  uint  totalts = _currentTimeStep+1;
+  H5Awrite(attr,H5T_NATIVE_UINT,&totalts);
+
+  H5Sclose(s);
+  H5Aclose(attr);  
+}
+
+
+int HDF5Common::GetNumTimeSteps()
+{
+  if (_file_id < 0) 
+  {
+    std::cerr<<"[ADIOS HDF5Error]: Invalid file to read timestep attribute."<<std::endl;
+    return -1;
+  }
+
+  if (_total_timestep <= 0) {
+    hid_t attr = H5Aopen(_file_id, "NumTimeSteps", H5P_DEFAULT);
+    
+    H5Aread(attr,H5T_NATIVE_UINT, &_total_timestep);
+    H5Aclose(attr);
+  }
+
+  return _total_timestep;
+}
+
+
+
+void HDF5Common::H5_Close() {
+    WriteTimeSteps();
+
+    H5Gclose(_group_id);
+    H5Fclose(_file_id);
+}
+
+void HDF5Common::H5_Advance(int totalts)
+{
+  _currentTimeStep++;
+  if (_currentTimeStep > 0) {
+    H5Gclose(_group_id);
+  }
+
+  std::string tsname="/TimeStep";
+  tsname.append(std::to_string(_currentTimeStep));
+
+  if (_writeMode) {
+      _group_id =
+	H5Gcreate2(_file_id, tsname.c_str(), H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+  } else {    
+    if ((totalts > 0) && (totalts <= _currentTimeStep)) 
+    {
+      return;
+    }
+    //std::cout<<" ... current  group "<<tsname.c_str()<<std::endl;
+    _group_id = 
+      H5Gopen(_file_id, tsname.c_str(), H5P_DEFAULT);
+  }
+}
+
+
+
+}

source/adios2/engine/hdf5/HDF5Common.h

+
+/*
+ * Distributed under the OSI-approved Apache License, Version 2.0.  See
+ * accompanying file Copyright.txt for details.
+ *
+ * HDF5CommonP.h
+ *
+ *  Created on: March 20, 2017
+ *      Author: Junmin
+ */
+
+#ifndef HDF5_COMMON_P_H_
+#define HDF5_COMMON_P_H_
+
+#include "core/Engine.h"
+#include "ADIOS_MPI.h"
+
+#include <hdf5.h>
+
+namespace adios
+{
+
+class HDF5Common 
+{
+
+public:
+    /**
+     * Constructor for HDF5 file 
+     * @param file name
+     */
+    HDF5Common();  
+
+    virtual ~HDF5Common();
+
+    void H5_Init(const std::string name, MPI_Comm m_MPIComm, bool toWrite);
+    void H5_Close();
+    void H5_Advance(int totalts);
+
+    int GetNumTimeSteps();    
+    void WriteTimeSteps();
+
+    hid_t _plist_id, _file_id; 
+    hid_t _group_id;
+   
+    hid_t DefH5T_COMPLEX_DOUBLE;
+    hid_t DefH5T_COMPLEX_FLOAT;
+    hid_t DefH5T_COMPLEX_LongDOUBLE;
+
+    int   _currentTimeStep;
+ private:
+    void H5_AdvanceWrite();    
+    bool _writeMode;
+    int _total_timestep;
+};
+
+} // end namespace adios
+
+#endif /* HDF5_COMMON_P_H_ */