added a class in testhdf5writeread.cpp

to read hdf directly

examples/hello/hdf5Writer/helloHDF5Writer.cpp

@@ -140,20 +140,27 @@ int main(int argc, char *argv[])
 	//HDF5Reader->InquireVariableDouble("wrongMyDoubles", true);
 	HDF5Reader->InquireVariableDouble(ioMyDoubles.m_Name, true);
 	*/
-	adios::HDF5Reader myReader(adios, "test.h5", "r", MPI_COMM_WORLD, HDF5Settings);
-	double values[15];
 
 #ifndef NEVER	
+	adios::HDF5Common myReader;
+	myReader.H5_Init("test.h5", MPI_COMM_WORLD, false);
+	double values[15];
 	ts = 0;
+
 	while (ts < totalts) {    
-	  myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);    
-	  myReader.Advance();
+	  //myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);    
+	  myReader.H5_Advance(totalts);
 	  ts++;
 	}
 
 #else
+	/*
+	adios::HDF5Reader myReader(adios, "test.h5", "r", MPI_COMM_WORLD, HDF5Settings);
+	double values[15];
+
 	myReader.ReadMe(ioMyDoubles, values, H5T_NATIVE_DOUBLE);
 	myReader.Close();
+	*/
 #endif
 
     }

source/adios2/engine/hdf5/HDF5Common.cpp

@@ -12,7 +12,7 @@
 
 #include <iostream> //needs to go away, this is just for demo purposes
 
-#include "adios2/ADIOSMPI.h"
+//#include "adios2/ADIOSMPI.h"
 
 namespace adios
 {
@@ -197,4 +197,96 @@ void HDF5Common::CheckWriteGroup()
     m_Group_id = H5Gcreate2(m_File_id, tsname.c_str(), H5P_DEFAULT, H5P_DEFAULT,
                             H5P_DEFAULT);
 }
+
+
+
+template <class T>
+void HDF5Common::ReadMe(Variable<T> &variable, T *data_array, hid_t h5type)
+{
+    hid_t datasetID =
+        H5Dopen(m_Group_id, variable.m_Name.c_str(), H5P_DEFAULT);
+
+#ifdef NEVER
+    if (_mpi_rank == 0)
+    {
+        std::cout << " hdf5 reading variable: " << variable.m_Name
+                  << " timestep: " << m_CurrentTimeStep << std::endl;
+    }
+#endif
+
+    if (datasetID < 0)
+    {
+        return;
+    }
+
+    hid_t filespace = H5Dget_space(datasetID);
+
+    if (filespace < 0)
+    {
+        return;
+    }
+
+    const int ndims = H5Sget_simple_extent_ndims(filespace);
+    hsize_t dims[ndims];
+    H5Sget_simple_extent_dims(filespace, dims, NULL);
+
+    // int dims_in = variable.m_GlobalDimensions.size();
+    variable.m_GlobalDimensions.clear();
+    for (int i = 0; i < ndims; i++)
+    {
+        variable.m_GlobalDimensions.push_back(dims[i]);
+    }
+
+    std::vector<hsize_t> count, offset, stride;
+
+    int elementsRead = 1;
+    for (int i = 0; i < ndims; i++)
+    {
+        if (variable.m_LocalDimensions.size() == ndims)
+        {
+            count.push_back(variable.m_LocalDimensions[i]);
+            elementsRead *= variable.m_LocalDimensions[i];
+        }
+        else
+        {
+            count.push_back(variable.m_GlobalDimensions[i]);
+            elementsRead *= variable.m_GlobalDimensions[i];
+        }
+
+        if (variable.m_Offsets.size() == ndims)
+        {
+            offset.push_back(variable.m_Offsets[i]);
+        }
+        else
+        {
+            offset.push_back(0);
+        }
+
+        stride.push_back(1);
+    }
+
+    hid_t ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset.data(),
+                                    stride.data(), count.data(), NULL);
+    if (ret < 0)
+    {
+        return;
+    }
+
+    hid_t mem_dataspace = H5Screate_simple(ndims, count.data(), NULL);
+
+    // T  data_array[elementsRead];
+    ret = H5Dread(datasetID, h5type, mem_dataspace, filespace, H5P_DEFAULT,
+                  data_array);
+
+    /* for (int i = 0; i < elementsRead; i++)
+    {
+        std::cout << "... ts " << m_CurrentTimeStep << ", "
+                  << data_array[i] << std::endl;
+    }
+    */
+    H5Sclose(mem_dataspace);
+
+    H5Sclose(filespace);
+    H5Dclose(datasetID);
+}
 }

source/adios2/engine/hdf5/HDF5Common.h

@@ -11,7 +11,7 @@
 #ifndef HDF5_COMMON_P_H_
 #define HDF5_COMMON_P_H_
 
-#include "adios2/ADIOSMPICommOnly.h"
+//#include "adios2/ADIOSMPICommOnly.h"
 #include "adios2/core/Engine.h"
 
 #include <hdf5.h>
@@ -38,6 +38,11 @@ public:
     int GetNumTimeSteps();
     void WriteTimeSteps();
 
+    template <class T>
+      void ReadMe(Variable<T> &variable, T *data_array, hid_t h5type);
+    
+    //void ReadFromHDF5(const char* name, void* data_array);
+
     hid_t m_Plist_id, m_File_id;
     hid_t m_Group_id;
 
@@ -50,7 +55,7 @@ public:
     void CheckWriteGroup();
 
 private:
-    void H5_AdvanceWrite();
+    //void H5_AdvanceWrite();
     bool m_WriteMode;
     int m_Total_timestep;
 };

source/adios2/engine/hdf5/HDF5ReaderP.cpp

@@ -149,52 +149,52 @@ HDF5Reader::InquireVariableDouble(const std::string &variableName, const bool)
         UseHDFRead(variableName, values, H5T_NATIVE_DOUBLE);
         Variable<double> v =
             m_ADIOS.DefineVariable<double>("junk", adios::Dims{8});
-        ReadMe(v, values, H5T_NATIVE_DOUBLE);
+        _H5File.ReadMe(v, values, H5T_NATIVE_DOUBLE);
 
         Variable<char> v1 =
             m_ADIOS.DefineVariable<char>("junk1", adios::Dims{8});
 
         char vv1[1];
-        ReadMe(v1, vv1, H5T_NATIVE_CHAR);
+        _H5File.ReadMe(v1, vv1, H5T_NATIVE_CHAR);
 
         Variable<unsigned char> v2 =
             m_ADIOS.DefineVariable<unsigned char>("junk2", adios::Dims{8});
         unsigned char vv2[1];
-        ReadMe(v2, vv2, H5T_NATIVE_UCHAR);
+        _H5File.ReadMe(v2, vv2, H5T_NATIVE_UCHAR);
 
         Variable<unsigned int> v3 =
             m_ADIOS.DefineVariable<unsigned int>("junk3", adios::Dims{8});
         unsigned int vv3[1];
-        ReadMe(v3, vv3, H5T_NATIVE_UINT);
+        _H5File.ReadMe(v3, vv3, H5T_NATIVE_UINT);
 
         Variable<int> v4 = m_ADIOS.DefineVariable<int>("junk4", adios::Dims{8});
         int vv4[1];
-        ReadMe(v4, vv4, H5T_NATIVE_INT);
+        _H5File.ReadMe(v4, vv4, H5T_NATIVE_INT);
 
         Variable<float> v5 =
             m_ADIOS.DefineVariable<float>("junk5", adios::Dims{8});
         float vv5[1];
-        ReadMe(v5, vv5, H5T_NATIVE_FLOAT);
+        _H5File.ReadMe(v5, vv5, H5T_NATIVE_FLOAT);
 
         Variable<short> v6 =
             m_ADIOS.DefineVariable<short>("junk6", adios::Dims{8});
         short vv6[1];
-        ReadMe(v6, vv6, H5T_NATIVE_SHORT);
+        _H5File.ReadMe(v6, vv6, H5T_NATIVE_SHORT);
 
         Variable<unsigned short> v7 =
             m_ADIOS.DefineVariable<unsigned short>("junk7", adios::Dims{8});
         unsigned short vv7[1];
-        ReadMe(v7, vv7, H5T_NATIVE_USHORT);
+        _H5File.ReadMe(v7, vv7, H5T_NATIVE_USHORT);
 
         Variable<long> v8 =
             m_ADIOS.DefineVariable<long>("junk8", adios::Dims{8});
         long vv8[1];
-        ReadMe(v8, vv8, H5T_NATIVE_LONG);
+        _H5File.ReadMe(v8, vv8, H5T_NATIVE_LONG);
 
         Variable<unsigned long> v9 =
             m_ADIOS.DefineVariable<unsigned long>("junk9", adios::Dims{8});
         unsigned long vv9[1];
-        ReadMe(v9, vv9, H5T_NATIVE_ULONG);
+        _H5File.ReadMe(v9, vv9, H5T_NATIVE_ULONG);
 
         if (_H5File.m_CurrentTimeStep >= totalts - 1)
         {
@@ -236,95 +236,6 @@ HDF5Reader::InquireVariableCompound(const std::string &variableName,
     return NULL;
 }
 
-template <class T>
-void HDF5Reader::ReadMe(Variable<T> &variable, T *data_array, hid_t h5type)
-{
-    hid_t datasetID =
-        H5Dopen(_H5File.m_Group_id, variable.m_Name.c_str(), H5P_DEFAULT);
-
-#ifdef NEVER
-    if (_mpi_rank == 0)
-    {
-        std::cout << " hdf5 reading variable: " << variable.m_Name
-                  << " timestep: " << _H5File.m_CurrentTimeStep << std::endl;
-    }
-#endif
-
-    if (datasetID < 0)
-    {
-        return;
-    }
-
-    hid_t filespace = H5Dget_space(datasetID);
-
-    if (filespace < 0)
-    {
-        return;
-    }
-
-    const int ndims = H5Sget_simple_extent_ndims(filespace);
-    hsize_t dims[ndims];
-    H5Sget_simple_extent_dims(filespace, dims, NULL);
-
-    // int dims_in = variable.m_GlobalDimensions.size();
-    variable.m_GlobalDimensions.clear();
-    for (int i = 0; i < ndims; i++)
-    {
-        variable.m_GlobalDimensions.push_back(dims[i]);
-    }
-
-    std::vector<hsize_t> count, offset, stride;
-
-    int elementsRead = 1;
-    for (int i = 0; i < ndims; i++)
-    {
-        if (variable.m_LocalDimensions.size() == ndims)
-        {
-            count.push_back(variable.m_LocalDimensions[i]);
-            elementsRead *= variable.m_LocalDimensions[i];
-        }
-        else
-        {
-            count.push_back(variable.m_GlobalDimensions[i]);
-            elementsRead *= variable.m_GlobalDimensions[i];
-        }
-
-        if (variable.m_Offsets.size() == ndims)
-        {
-            offset.push_back(variable.m_Offsets[i]);
-        }
-        else
-        {
-            offset.push_back(0);
-        }
-
-        stride.push_back(1);
-    }
-
-    hid_t ret = H5Sselect_hyperslab(filespace, H5S_SELECT_SET, offset.data(),
-                                    stride.data(), count.data(), NULL);
-    if (ret < 0)
-    {
-        return;
-    }
-
-    hid_t mem_dataspace = H5Screate_simple(ndims, count.data(), NULL);
-
-    // T  data_array[elementsRead];
-    ret = H5Dread(datasetID, h5type, mem_dataspace, filespace, H5P_DEFAULT,
-                  data_array);
-
-    /* for (int i = 0; i < elementsRead; i++)
-    {
-        std::cout << "... ts " << _H5File.m_CurrentTimeStep << ", "
-                  << data_array[i] << std::endl;
-    }
-    */
-    H5Sclose(mem_dataspace);
-
-    H5Sclose(filespace);
-    H5Dclose(datasetID);
-}
 
 template <class T>
 void HDF5Reader::UseHDFRead(const std::string &variableName, T *values,

source/adios2/engine/hdf5/HDF5ReaderP.h

@@ -110,12 +110,13 @@ public:
 
     void Close(const int transportIndex = -1);
 
-    template <class T>
+    template <typename T>
     void UseHDFRead(const std::string &variableName, T *values, hid_t h5type);
 
+    /*
     template <class T>
     void ReadMe(Variable<T> &variable, T *values, hid_t h5type);
-
+    */
 private:
     HDF5Common _H5File;
     void Init();