change HDF5's file open options to close all sub-file objects when a file is closed

[Roland Haas]

this is strictly speaking not necessary, since any need for it is caused by a HDF5 object leak. On the other hand it does not hurt either additionally one could overload H5Fclose and warn the user when there are still open objects when a file is closed, ie:

//////////////////////////////////////////////////////////////////////////////
 // Close HDF5 file checking for leaked objects
 //////////////////////////////////////////////////////////////////////////////
 static herr_t H5Fclose (hid_t file)
 {
   DECLARE_CCTK_PARAMETERS;

   herr_t retval;
   int error_count = 0;

   hsize_t objectcount;
   HDF5_ERROR (objectcount = H5Fget_obj_count(file,
                                              H5F_OBJ_ALL | H5F_OBJ_LOCAL));
   if (objectcount > 1) {
     std::vector<char> fn;
     hsize_t sz_fn;

     HDF5_ERROR (sz_fn = H5Fget_name(file, NULL, 0));
     fn.resize(sz_fn+1);
     HDF5_ERROR (H5Fget_name(file, &fn[0], fn.size()));

     CCTK_VWarn (1, __LINE__, __FILE__, CCTK_THORNSTRING,
                 "%d open HDF5 objects when closing file '%s'",
                 int(objectcount)-1, &fn[0]);
   }
   HDF5_ERROR (retval = ::H5Fclose (file));

   return retval;
 }

Keyword: CarpetIOHDF5

[Erik Schnetter]

I assume this will help reduce memory usage for HDF5. Please apply.

[Roland Haas]

I applied the patch (but not the overloaded HDF5 close function) as Carpet hash f0dc71726af0 "CarpetIOHDF5: close all HDF5 objects when closing a file".