Merge pull request #2459 from guj/issue2376

added support for APPEND in HDF5 engine
ornladios · Sep 15, 2020 · 2baa08d · 2baa08d
2 parents b046337 + 771231a
commit 2baa08d
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Showing 7 changed files with 469 additions and 5 deletions.
diff --git a/source/adios2/engine/hdf5/HDF5ReaderP.cpp b/source/adios2/engine/hdf5/HDF5ReaderP.cpp
@@ -372,6 +372,7 @@ void HDF5ReaderP::DoClose(const int transportIndex)
     m_H5File.Close();
 }
 
+size_t HDF5ReaderP::DoSteps() const { return m_H5File.GetAdiosStep(); }
 } // end namespace engine
 } // end namespace core
 } // end namespace adios2
diff --git a/source/adios2/engine/hdf5/HDF5ReaderP.h b/source/adios2/engine/hdf5/HDF5ReaderP.h
@@ -97,6 +97,8 @@ class HDF5ReaderP : public Engine
     void UseHDFRead(Variable<T> &variable, T *values, hid_t h5Type);
 
     std::vector<std::string> m_DeferredStack;
+
+    size_t DoSteps() const final;
 };
 
 } // end namespace engine

diff --git a/source/adios2/engine/hdf5/HDF5WriterP.cpp b/source/adios2/engine/hdf5/HDF5WriterP.cpp
@@ -74,13 +74,25 @@ void HDF5WriterP::Init()
     {
         // is a file with .bp ending
         std::string updatedName = m_Name.substr(0, wpos) + suffix;
-        m_H5File.Init(updatedName, m_Comm, true);
+        if (m_OpenMode == Mode::Append)
+            m_H5File.Append(updatedName, m_Comm);
+        else
+            m_H5File.Init(updatedName, m_Comm, true);
     }
     else
     {
-        m_H5File.Init(m_Name, m_Comm, true);
+        if (m_OpenMode == Mode::Append)
+            m_H5File.Append(m_Name, m_Comm);
+        else
+            m_H5File.Init(m_Name, m_Comm, true);
     }
     m_H5File.ParseParameters(m_IO);
+
+    if (m_OpenMode == Mode::Append)
+    {
+        m_H5File.ReadAttrToIO(m_IO);
+        m_H5File.ReadAllVariables(m_IO);
+    }
 #endif
 }
 

diff --git a/source/adios2/toolkit/interop/hdf5/HDF5Common.cpp b/source/adios2/toolkit/interop/hdf5/HDF5Common.cpp
@@ -135,6 +135,52 @@ void HDF5Common::ParseParameters(core::IO &io)
     }
 }
 
+void HDF5Common::Append(const std::string &name, helper::Comm const &comm)
+{
+    m_PropertyListId = H5Pcreate(H5P_FILE_ACCESS);
+
+    if (MPI_API const *mpi = GetHDF5Common_MPI_API())
+    {
+        if (mpi && mpi->init(comm, m_PropertyListId, &m_CommRank, &m_CommSize))
+        {
+            m_MPI = mpi;
+        }
+    }
+
+    m_FileId = H5Fopen(name.c_str(), H5F_ACC_RDWR, m_PropertyListId);
+    H5Pclose(m_PropertyListId);
+
+    std::string ts0;
+    StaticGetAdiosStepString(ts0, 0);
+
+    if (m_FileId >= 0)
+    {
+        if (H5Lexists(m_FileId, ts0.c_str(), H5P_DEFAULT) != 0)
+        {
+            m_IsGeneratedByAdios = true;
+        }
+        if (!m_IsGeneratedByAdios)
+            throw std::ios_base::failure(
+                "HDF5Engine Append error. Likely no such file." + name);
+
+        GetNumAdiosSteps(); // read how many steps exists in this file
+
+        if (0 == m_NumAdiosSteps)
+            throw std::ios_base::failure(
+                "HDF5Engine Append error. No valid steps found in " + name);
+        if (1 == m_NumAdiosSteps)
+            m_GroupId = H5Gopen(m_FileId, ts0.c_str(), H5P_DEFAULT);
+        else
+            SetAdiosStep(m_NumAdiosSteps - 1);
+
+        m_WriteMode = true;
+        Advance();
+    }
+    else
+        throw std::ios_base::failure(
+            "HDF5Engine Append error. Likely no such file." + name);
+}
+
 void HDF5Common::Init(const std::string &name, helper::Comm const &comm,
                       bool toWrite)
 {
@@ -204,9 +250,13 @@ void HDF5Common::WriteAdiosSteps()
     }
 
     hid_t s = H5Screate(H5S_SCALAR);
-    hid_t attr =
-        H5Acreate(m_FileId, ATTRNAME_NUM_STEPS.c_str(),
-                  /*"NumSteps",*/ H5T_NATIVE_UINT, s, H5P_DEFAULT, H5P_DEFAULT);
+    hid_t attr = H5Aexists(m_FileId, ATTRNAME_NUM_STEPS.c_str());
+    if (0 == attr)
+        attr = H5Acreate(m_FileId, ATTRNAME_NUM_STEPS.c_str(), H5T_NATIVE_UINT,
+                         s, H5P_DEFAULT, H5P_DEFAULT);
+    else
+        attr = H5Aopen(m_FileId, ATTRNAME_NUM_STEPS.c_str(), H5P_DEFAULT);
+
     unsigned int totalAdiosSteps = m_CurrentAdiosStep + 1;
 
     if (m_GroupId < 0)
@@ -220,6 +270,8 @@ void HDF5Common::WriteAdiosSteps()
     H5Aclose(attr);
 }
 
+unsigned int HDF5Common::GetAdiosStep() const { return m_NumAdiosSteps; }
+
 unsigned int HDF5Common::GetNumAdiosSteps()
 {
     if (m_WriteMode)

diff --git a/source/adios2/toolkit/interop/hdf5/HDF5Common.h b/source/adios2/toolkit/interop/hdf5/HDF5Common.h
@@ -127,6 +127,7 @@ class HDF5Common
 
     void ParseParameters(core::IO &io);
     void Init(const std::string &name, helper::Comm const &comm, bool toWrite);
+    void Append(const std::string &name, helper::Comm const &comm);
 
     template <class T>
     void Write(core::Variable<T> &variable, const T *values);
@@ -172,6 +173,7 @@ class HDF5Common
     void SetAdiosStep(int ts);
 
     unsigned int GetNumAdiosSteps();
+    unsigned int GetAdiosStep() const;
     void WriteAdiosSteps();
 
     void ReadVariables(unsigned int ts, core::IO &io);

diff --git a/testing/adios2/engine/hdf5/CMakeLists.txt b/testing/adios2/engine/hdf5/CMakeLists.txt
@@ -23,6 +23,10 @@ gtest_add_tests_helper(WriteMemorySelectionRead  ${hdf5_mpi}
   HDF5 Engine.HDF5. ""
 )
 
+gtest_add_tests_helper(Append  ${hdf5_mpi}
+  HDF5 Engine.HDF5. ""
+)
+
 gtest_add_tests_helper(NativeHDF5WriteRead ${hdf5_mpi} "" Engine.HDF5. "")
 if(HDF5_C_INCLUDE_DIRS)
   target_include_directories(Test.Engine.HDF5.NativeHDF5WriteRead${hdf5_sfx}