Merge remote-tracking branch 'gh/develop' into feature/gunney/blueprint-mesh-shaping

Author: gunney1

src/axom/sidre/core/Group.cpp

@@ -2266,7 +2266,7 @@ bool Group::load(const hid_t& h5_id,
  *
  * Load External Data from an hdf5 file
  *
- * Note: this ASSUMES uses the "sidre_hdf5" protocol
+ * Note: this ASSUMES usage of the "sidre_hdf5" protocol
  *************************************************************************
  */
 bool Group::loadExternalData(const hid_t& h5_id)
@@ -2281,6 +2281,38 @@ bool Group::loadExternalData(const hid_t& h5_id)
   return !(getDataStore()->getConduitErrorOccurred());
 }
 
+/*
+ *************************************************************************
+ *
+ * Load External Data from a path within an hdf5 file
+ *
+ * Note: this ASSUMES usage of the "sidre_hdf5" protocol
+ *************************************************************************
+ */
+bool Group::loadExternalData(const hid_t& h5_id, const std::string& group_path)
+{
+  bool success;
+  std::string delim(1, getPathDelimiter());
+  if(group_path.empty() || group_path == delim)
+  {
+    // An empty or trivial path means the load should read from the start of
+    // the file.
+    success = loadExternalData(h5_id);
+  }
+  else
+  {
+    Node n;
+    createExternalLayout(n);
+    ConduitErrorSuppressor checkConduitCall(getDataStore());
+
+    std::string read_path("sidre/external/" + group_path);
+
+    checkConduitCall([&] { conduit::relay::io::hdf5_read(h5_id, read_path, n); });
+    success = !(getDataStore()->getConduitErrorOccurred());
+  }
+  return success;
+}
+
 #endif /* AXOM_USE_HDF5 */
 
 ////////////////////////////////////////////////////////////////////////

src/axom/sidre/core/Group.hpp

@@ -1650,7 +1650,7 @@ class Group
             std::string& name_from_file);
 
   /*!
-   * \brief Load data into the Group's external views from a hdf5 handle.
+   * \brief Load data into the Group's external views from an hdf5 handle.
    *
    * No protocol argument is needed, as this only is used with the sidre_hdf5
    * protocol.  Returns true (success) if no Conduit I/O error occurred since
@@ -1662,6 +1662,22 @@ class Group
    */
   bool loadExternalData(const hid_t& h5_id);
 
+  /*!
+   * \brief Load data into the Group's external views from a path into
+   *        hdf5 handle
+   *
+   * No protocol argument is needed, as this only is used with the sidre_hdf5
+   * protocol.  Returns true (success) if no Conduit I/O error occurred since
+   * this Group's DataStore was created or had its error flag cleared; false,
+   * if an error occurred at some point.
+   *
+   * \param h5_id        hdf5 handle
+   * \param group_path   Path pointing to this Group. This path must be the
+   *                     relative path from the top Group that was written
+   *                     to a file to this Group.
+   */
+  bool loadExternalData(const hid_t& h5_id, const std::string& group_path);
+
 #endif /* AXOM_USE_HDF5 */
 
   //@}

src/axom/sidre/spio/IOManager.cpp

@@ -465,6 +465,161 @@ void IOManager::loadExternalData(sidre::Group* datagroup,
   (void)m_baton->pass();
 }
 
+void IOManager::loadExternalData(sidre::Group* parent_group,
+                                 sidre::Group* load_group,
+                                 const std::string& root_file)
+{
+  int num_files = getNumFilesFromRoot(root_file);
+  int num_groups = getNumGroupsFromRoot(root_file);
+  SLIC_ASSERT(num_files > 0);
+  SLIC_ASSERT(num_groups > 0);
+
+  if(m_baton)
+  {
+    if(m_baton->getNumFiles() != num_files)
+    {
+      delete m_baton;
+      m_baton = nullptr;
+    }
+  }
+
+  if(!m_baton)
+  {
+    m_baton = new IOBaton(m_mpi_comm, num_files, num_groups);
+  }
+
+#ifdef AXOM_USE_HDF5
+  std::string file_pattern = getHDF5FilePattern(root_file);
+
+  std::string parent_name(parent_group->getPathName());
+  std::string load_name(load_group->getPathName());
+  axom::Path parent_path(parent_name);
+  axom::Path load_path(load_name);
+  std::vector<std::string> parent_parts(parent_path.parts());
+  std::vector<std::string> load_parts(load_path.parts());
+
+  size_t parent_size = parent_parts.size();
+  bool can_load = true;
+  if(load_parts.size() < parent_size)
+  {
+    can_load = false;
+  }
+
+  for(size_t i = 0; i < parent_size; ++i)
+  {
+    if(parent_parts[i] != load_parts[i])
+    {
+      can_load = false;
+    }
+  }
+
+  std::string subpath = load_name.substr(parent_name.size());
+  char delimiter = parent_group->getPathDelimiter();
+  if(!subpath.empty() && subpath[0] == delimiter)
+  {
+    subpath.erase(0, 1);
+  }
+
+  if(!subpath.empty() && !parent_group->hasGroup(subpath))
+  {
+    can_load = false;
+  }
+
+  int set_id = m_baton->wait();
+
+  if(can_load)
+  {
+    if(num_groups <= m_comm_size)
+    {
+      if(m_my_rank < num_groups)
+      {
+        herr_t errv;
+        AXOM_UNUSED_VAR(errv);
+
+        std::string hdf5_name =
+          getFileNameForRank(file_pattern, root_file, set_id);
+
+        hdf5_name = getSCRPath(hdf5_name);
+
+        hid_t h5_file_id = conduit::relay::io::hdf5_open_file_for_read(hdf5_name);
+        SLIC_ASSERT(h5_file_id >= 0);
+
+        std::string group_name = "datagroup";
+        if(H5Lexists(h5_file_id, group_name.c_str(), 0) <= 0)
+        {
+          group_name = fmt::sprintf("datagroup_%07d", m_my_rank);
+        }
+
+        hid_t h5_group_id = H5Gopen(h5_file_id, group_name.c_str(), 0);
+        SLIC_ASSERT(h5_group_id >= 0);
+
+        load_group->loadExternalData(h5_group_id, subpath);
+
+        errv = H5Gclose(h5_group_id);
+        SLIC_ASSERT(errv >= 0);
+
+        errv = H5Fclose(h5_file_id);
+        SLIC_ASSERT(errv >= 0);
+      }
+    }
+    else
+    {
+      for(int input_rank = m_my_rank; input_rank < num_groups;
+          input_rank += m_comm_size)
+      {
+        herr_t errv;
+        AXOM_UNUSED_VAR(errv);
+
+        std::string hdf5_name =
+          getFileNameForRank(file_pattern, root_file, input_rank);
+
+        hdf5_name = getSCRPath(hdf5_name);
+
+        hid_t h5_file_id = conduit::relay::io::hdf5_open_file_for_read(hdf5_name);
+        SLIC_ASSERT(h5_file_id >= 0);
+
+        std::string group_name = "datagroup";
+        if(H5Lexists(h5_file_id, group_name.c_str(), 0) <= 0)
+        {
+          group_name = fmt::sprintf("datagroup_%07d", input_rank);
+        }
+
+        hid_t h5_group_id = H5Gopen(h5_file_id, group_name.c_str(), 0);
+        SLIC_ASSERT(h5_group_id >= 0);
+
+        std::string input_name = fmt::sprintf("rank_%07d", input_rank);
+
+        input_name = input_name + delimiter + "sidre_input" + delimiter + subpath;
+
+        Group* one_rank_input = parent_group->getGroup(input_name);
+
+        one_rank_input->loadExternalData(h5_group_id, subpath);
+
+        errv = H5Gclose(h5_group_id);
+        SLIC_ASSERT(errv >= 0);
+
+        errv = H5Fclose(h5_file_id);
+        SLIC_ASSERT(errv >= 0);
+      }
+    }
+  }
+  else
+  {
+    SLIC_WARNING("Path from parent group "
+                 << parent_group->getPathName() << " to group "
+                 << load_group->getPathName()
+                 << " was not found. No external data will be loaded.");
+  }
+
+#else
+  AXOM_UNUSED_VAR(datagroup);
+  SLIC_WARNING("Loading external data only only available "
+               << "when Axom is configured with hdf5");
+#endif /* AXOM_USE_HDF5 */
+
+  (void)m_baton->pass();
+}
+
 /*
  *************************************************************************
  *

src/axom/sidre/spio/IOManager.hpp

@@ -289,11 +289,48 @@ class IOManager
    * This currently only works if the root file was created for protocol
    * sidre_hdf5.
    *
+   * The call to this method must follow a call to the IOManager::read with the
+   * same group and root file.
+   *
+   * This is intended as the third step of the three step process to load
+   * external data.  The first step is the call to IOManager::read; the
+   * second step is to set valid pointers on all external views in the
+   * hierarchy under the passed-in group; the third step is the call to
+   * this method.
+   *
    * \param group         Group to fill with external data from input
    * \param root_file     root file containing input data
    */
   void loadExternalData(sidre::Group* group, const std::string& root_file);
 
+  /*!
+   * \brief piecewise load of external data into a group
+   *
+   * This currently only works if the root file was created for protocol
+   * sidre_hdf5.
+   *
+   * This is intended as an alternative way to load external data, in a
+   * piecewise manner rather than loading all external data of a Sidre
+   * hierarchy at once.  load_group is a Group somewhere in the hierarchy
+   * under parent_group, and only the external data for views in the
+   * subtree under load_group will be loaded.  In the second step of the
+   * three step process, the calling code should set valid pointers on all
+   * external views in the subtree under load_group.  The third step is
+   * to call this method.  parent_group must be the same group that was
+   * passed to IOManager::read with the same root file.
+   *
+   * This method may be called multiple times with different instances of
+   * load_group representing different subtrees of the hierachy under
+   * parent_group.
+   *
+   * \param parent_group  Group that was passed to IOManager::read
+   * \param load_group    Group holding views to be filled with external data
+   * \param root_file     root file containing input data
+   */
+  void loadExternalData(sidre::Group* parent_group,
+                        sidre::Group* load_group,
+                        const std::string& root_file);
+
   /*!
    * \brief gets the number of files in the dataset from the specified root file
    */