Serial File I/O

Sidre provides for file I/O to HDF5 files and file handles and to JSON files. Serial I/O is accomplished using methods of the Group class; parallel I/O is done using the IOManager class.

HDF5 is an optional dependency for Sidre. Sidre APIs that rely on HDF5 will be available only if Sidre was compiled with HDF5 support. The symbol that controls dependency on HDF5 is AXOM_USE_HDF5, defined in the source file axom/config.hpp.

File I/O using Group class

The Group class contains the save(), load(), and loadExternalData() methods. Each method can be called with a file name or an HDF5 handle. The save() and load() methods allow the code to specify a protocol, specifying how the operation should be performed and what file format should be used. The loadExternalData() method takes no protocol argument since it is only used with the sidre_hdf5 protocol. The save() method can also take a pointer to an Attribute object. If that Attribute pointer is null, all Views are saved, but if an Attribute pointer is provided, only Views with that Attribute explicitly set will be saved.

Insert a link to Doxygen for Group, and mention that protocols are listed here.

The load() method retrieves the hierarchical data structure stored in the file or pointer, and instantiates Groups, Views and Attributes to represent the structure rooted in this Group. By default, the contents of this Group are destroyed prior to reading the file’s contents. This can be suppressed by passing true as the preserve_contents argument to load(), resulting in the current Group’s subtree being merged with the file’s contents.

Usage of save() and load() is shown in the following example.

  // Save the data store to a file,
  // saving all Views
  ds->getRoot()->save(filename, protocol);
  // Delete the data hierarchy under the root, then load it from the file
  ds->getRoot()->load(filename, protocol);
  Group* additional = ds->getRoot()->createGroup("additional");
  // Load another copy of the data store into the "additional" group
  // without first clearing all its contents
  std::string groupname;
  additional->load(filename, protocol, true, groupname);

The loadExternalData() method is used to read “external” data from an HDF5 file created with the sidre_hdf5 protocol. This is data referred to by Views that is not stored in Sidre Buffers but in a raw pointer.

The overloads of save() and load() that take HDF5 handles and the loadExternalData() method are public APIs that are used to implement parallel I/O through the IOManager class.