Merge pull request #329 from guj/1204

added GetPreferred for stream reading

examples/heatTransfer/write/IO_h5mixer.cpp

@@ -32,8 +32,17 @@ adios2::Variable<unsigned int> *varGndx = nullptr;
 IO::IO(const Settings &s, MPI_Comm comm)
 {
     rank_saved = s.rank;
-    // m_outputfilename = s.outputfile + ".h5";
+
     m_outputfilename = s.outputfile;
+    std::string suffix = ".h5";
+
+    int ss = s.outputfile.size();
+    if ((ss > suffix.size()) && s.outputfile.find(suffix) != ss - suffix.size())
+    {
+        // Your code here
+        m_outputfilename += suffix;
+    }
+
     /*ad = new adios2::ADIOS(std::string(DEFAULT_CONFIG_STR), comm,
                            adios2::DebugON);
     */

examples/heatTransfer/write/IO_ph5.cpp

@@ -276,7 +276,18 @@ std::shared_ptr<HDF5NativeWriter> h5writer;
 
 IO::IO(const Settings &s, MPI_Comm comm)
 {
-    m_outputfilename = s.outputfile + ".h5";
+    std::string suffix = ".h5";
+    m_outputfilename = s.outputfile + suffix;
+
+    int ss = s.outputfile.size();
+    int pos = s.outputfile.find(suffix);
+    if ((ss > suffix.size()) && (pos == ss - suffix.size()))
+    {
+        // Your code here
+        m_outputfilename = s.outputfile;
+    }
+
+    //    m_outputfilename = s.outputfile + ".h5";
 
     if (s.outputfile[0] == '0')
     {

examples/heatTransfer/write/IO_ph5_adios2.cpp

@@ -21,7 +21,17 @@ adios2::Variable<unsigned int> *varGndx = nullptr;
 
 IO::IO(const Settings &s, MPI_Comm comm)
 {
-    m_outputfilename = s.outputfile + ".h5";
+    std::string suffix = ".h5";
+    m_outputfilename = s.outputfile + suffix;
+
+    int ss = s.outputfile.size();
+    int pos = s.outputfile.find(suffix);
+    if ((ss > suffix.size()) && (pos == ss - suffix.size()))
+    {
+        // Your code here
+        m_outputfilename = s.outputfile;
+    }
+
     ad = new adios2::ADIOS(comm, adios2::DebugOFF);
 
     // Define method for engine creation

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 +230,50 @@ 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