added GetPreferred for stream reading

source/adios2/engine/hdf5/HDF5ReaderP.cpp

@@ -74,9 +74,16 @@ void HDF5ReaderP::UseHDFRead(Variable<T> &variable, T *data, hid_t h5Type)
 {
     int ts = 0;
     T *values = data;
+    size_t variableStart = variable.m_StepsStart;
+    if (!m_InStreamMode && (variableStart == 1))
+    { // variableBase::m_StepsStart min=1
+        variableStart = 0;
+    }
+
     while (ts < variable.m_StepsCount)
     {
-        m_H5File.SetTimeStep(variable.m_StepsStart + ts);
+        // m_H5File.SetTimeStep(variable.m_StepsStart + ts);
+        m_H5File.SetTimeStep(variableStart + ts);
 
         hid_t dataSetId =
             H5Dopen(m_H5File.m_GroupId, variable.m_Name.c_str(), H5P_DEFAULT);
@@ -223,7 +230,43 @@ values); #endif
 }
 */
 
-void HDF5ReaderP::EndStep() { m_H5File.Advance(); }
+StepStatus HDF5ReaderP::BeginStep(StepMode mode, const float timeoutSeconds) 
+{
+  m_InStreamMode=true;
+  int ts = m_H5File.GetNumTimeSteps();  
+  if (m_StreamAt >= ts) {
+    return StepStatus::EndOfStream;
+  }
+
+  return StepStatus::OK;
+}
+
+void HDF5ReaderP::EndStep() {   m_StreamAt ++; m_H5File.Advance(); }
+
+void HDF5ReaderP::PerformGets()
+{
+  if (!m_InStreamMode) {
+    throw std::runtime_error("PerformGets() needs to follow stream read sequeuences.");
+  }
+
+#define declare_type(T)                                                        \
+    for (std::string variableName : m_DeferredStack) { \
+        Variable<T>* var = m_IO.InquireVariable<T>(variableName);         \
+        if (var  != nullptr)					       \
+	  {                                                                    \
+	    var->m_StepsStart = m_StreamAt;                               \
+            var->m_StepsCount = 1;				\
+	    hid_t h5Type = m_H5File.GetHDF5Type<T>();                          \
+	    UseHDFRead(*var, var->GetData(), h5Type);	\
+	    break;						\
+	  } \
+    }    
+ADIOS2_FOREACH_TYPE_1ARG(declare_type)
+#undef declare_type  
+
+
+  m_DeferredStack.clear();
+}
 
 void HDF5ReaderP::Close(const int transportIndex) { m_H5File.Close(); }
 

source/adios2/engine/hdf5/HDF5ReaderP.h

@@ -36,8 +36,11 @@ public:
 
     bool IsValid();
 
+    StepStatus BeginStep(StepMode mode, const float timeoutSeconds = 0.f) final;
     void EndStep() final;
 
+    void PerformGets() final;
+
     void Close(const int transportIndex = -1) final;
 
 private:
@@ -45,6 +48,7 @@ private:
     void Init() final;
 
     bool m_InStreamMode = false; // default is not streaming
+    unsigned int m_StreamAt = 0; // stream step counter
 #define declare_type(T)                                                        \
     void DoGetSync(Variable<T> &, T *) final;                                  \
     void DoGetDeferred(Variable<T> &, T *) final;                              \
@@ -62,6 +66,8 @@ private:
     // void UseHDFRead(const std::string &variableName, T *values, hid_t
     // h5Type);
     void UseHDFRead(Variable<T> &variable, T *values, hid_t h5Type);
+
+    std::vector<std::string> m_DeferredStack;
 };
 };
 #endif /* ADIOS2_ENGINE_HDF5_HDF5READERP_H_ */

source/adios2/engine/hdf5/HDF5ReaderP.tcc

@@ -33,10 +33,21 @@ void HDF5ReaderP::GetSyncCommon(Variable<T> &variable, T *data)
 template <class T>
 void HDF5ReaderP::GetDeferredCommon(Variable<T> &variable, T *data)
 {
+#ifdef NEVER
     // returns immediately
     // m_HDF53Deserializer.GetDeferredVariable(variable, data);
 
-    throw std::runtime_error("Todo: GetDefCommon");
+    if (m_InStreamMode)
+    {
+        variable.m_StepsStart = m_StreamAt; // current step
+        variable.m_StepsCount = 1;
+    }
+    hid_t h5Type = m_H5File.GetHDF5Type<T>();
+    UseHDFRead(variable, data, h5Type);
+#else
+    m_DeferredStack.push_back(variable.m_Name);
+    variable.SetData(data);
+#endif
 }
 
 } // end namespace adios2