Merge pull request #3557 from dmitry-ganyushin/group-API-cleanup

Refactoring and clean-up group API

bindings/CXX11/adios2/cxx11/Group.cpp

@@ -21,17 +21,6 @@ Group Group::InquireGroup(std::string group_name)
     auto m = m_Group->InquireGroup(group_name);
     return Group(m);
 }
-void Group::PrintTree()
-{
-    m_Group->PrintTree();
-    return;
-}
-
-void Group::BuildTree()
-{
-    m_Group->BuildTree();
-    return;
-}
 std::vector<std::string> Group::AvailableVariables()
 {
     return m_Group->AvailableVariables();
@@ -45,11 +34,6 @@ std::vector<std::string> Group::AvailableGroups()
     return m_Group->AvailableGroups();
 }
 
-std::map<std::string, std::set<std::string>> &Group::getTreeMap()
-{
-    return m_Group->getTreeMap();
-}
-
 std::string Group::InquirePath() { return m_Group->InquirePath(); }
 
 void Group::setPath(std::string path) { m_Group->setPath(path); }
@@ -64,7 +48,8 @@ DataType Group::AttributeType(const std::string &name) const
     helper::CheckForNullptr(m_Group, "in call to IO::AttributeType");
     return m_Group->InquireAttributeType(name);
 }
-Group::~Group(){};
+Group::~Group() = default;
+;
 // Explicit declaration of the public template methods
 // Limits the types
 #define declare_template_instantiation(T)                                      \

bindings/CXX11/adios2/cxx11/Group.h

@@ -39,23 +39,11 @@ class Group
 {
     friend class IO;
 
-private:
     Group(core::Group *group);
     core::Group *m_Group = nullptr;
 
 public:
     ~Group();
-    /**
-     * @brief Builds map that represents tree structure from m_Variable and
-     * m_Attributes from IO class
-     * @param
-     */
-    void BuildTree();
-    /**
-     * @brief Prints map that represents tree structure
-     * @param
-     */
-    void PrintTree();
     /**
      * @brief returns available groups on the path set
      * @param
@@ -91,11 +79,6 @@ class Group
      * @return new group object
      */
     Group InquireGroup(std::string group_name);
-    /**
-     * @brief returns  a reference to the map representing the tree stucture
-     * @param delimiter symbol
-     */
-    std::map<std::string, std::set<std::string>> &getTreeMap();
     /**
      * @brief Gets an existing variable of primitive type by name. A wrapper for
      * the corresponding function of the IO class

docs/user_guide/source/ecosystem/h5vol/vol.rst

@@ -5,7 +5,7 @@ Disclaimer
 
 The Virtual Object Layer (VOL) is a feature introduced in recent release of  HDF5 1.12 (https://hdf5.wiki/index.php/New_Features_in_HDF5_Release_1.12). 
 
-So please do make sure your HDF5 version supports VOL. 
+So please do make sure your HDF5 version supports the latest VOL. 
 
 Once the ADIOS VOL is compiled, There are two ways to apply it: 
 
@@ -70,4 +70,4 @@ Internal
 
 
 
-
+

docs/user_guide/source/engines/hdf5.rst

@@ -28,3 +28,15 @@ We can  pass options to HDF5 API from  ADIOS xml configuration. Currently we sup
 	<parameter key="H5ChunkVar" value="VarName1 VarName2"/>
 
 We suggest to read HDF5 documentation before appling these options.
+
+After the subfile feature is introduced  in HDF5 version 1.14, the ADIOS2 HDF5 engine will use subfiles as the default h5 format as it improves I/O in general (for example, see https://escholarship.org/uc/item/6fs7s3jb)
+
+To use the subfile feature, client needs to support MPI_Init_thread with MPI_THREAD_MULTIPLE. 
+
+Useful parameters from the  HDF lirbary to tune subfiles are:
+.. code-block:: xml
+		
+H5FD_SUBFILING_IOC_PER_NODE (num of subfiles per node)
+    set H5FD_SUBFILING_IOC_PER_NODE to 0 if the regular h5 file is prefered, before using ADIOS2 HDF5 engine. 
+H5FD_SUBFILING_STRIPE_SIZE
+H5FD_IOC_THREAD_POOL_SIZE

examples/CMakeLists.txt

@@ -22,3 +22,10 @@ endif()
 if(ADIOS2_HAVE_CUDA OR ADIOS2_HAVE_Kokkos_CUDA)
   add_subdirectory(cuda)
 endif()
+
+
+if(ADIOS2_HAVE_MPI AND ADIOS2_HAVE_HDF5)
+  if(HDF5_VERSION VERSION_GREATER_EQUAL 1.14)
+    add_subdirectory(h5subfile)
+  endif()
+endif()

examples/h5subfile/CMakeLists.txt

@@ -0,0 +1,10 @@
+#------------------------------------------------------------------------------#
+# Distributed under the OSI-approved Apache License, Version 2.0.  See
+# accompanying file Copyright.txt for details.
+#------------------------------------------------------------------------------#
+
+if(ADIOS2_HAVE_MPI)
+  add_executable(H5EngineSubfileTest h5_subfile.cpp)
+  target_link_libraries(H5EngineSubfileTest adios2::cxx11_mpi MPI::MPI_C)
+endif()
+