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Loading H5T_ARRAY data using load -hdf5


From: Rhys Ulerich
Subject: Loading H5T_ARRAY data using load -hdf5
Date: Fri, 18 Feb 2011 17:01:45 -0600

'Evening,

I've got some three dimensional HDF5 data of type H5T_ARRAY { [2]
H5T_IEEE_F64LE }.  At each (i,j,k) location this mean's I've got an
array of two floating point values.  Trying to use load to read the
data dies in HDF5 underneath Octave due to (it appears) the H5T_ARRAY
not being supported.  Can anyone recommend a way to pull such data
into Octave?

Some h5dump details and the specific error message from Octave follows.

Thanks in advance,
Rhys

[325 address@hidden sz-gcc-debug]$ h5dump -d /rho restart0.h5
HDF5 "restart0.h5" {
DATASET "/rho" {
COMMENT "Nondimensional density coefficient stored row-majo"
   DATATYPE  H5T_ARRAY { [2] H5T_IEEE_F64LE }
   DATASPACE  SIMPLE { ( 1, 1, 16 ) / ( 1, 1, 16 ) }
   DATA {
   (0,0,0): [ 1, 0 ], [ 1, 0 ], [ 1, 0 ], [ 1, 0 ], [ 1, 0 ], [ 1, 0 ],
   (0,0,6): [ 1, 0 ], [ 1, 0 ], [ 1, 0 ], [ 1, 0 ], [ 1, 0 ], [ 1, 0 ],
   (0,0,12): [ 1, 0 ], [ 1, 0 ], [ 1, 0 ], [ 1, 0 ]
   }
   ATTRIBUTE "esio_field_metadata" {
      DATATYPE  H5T_STD_I32LE
      DATASPACE  SIMPLE { ( 8 ) / ( 8 ) }
      DATA {
      (0): 0, 1, 3, 0, 1, 1, 16, 2
      }
   }
}
}

octave:1> load "restart0.h5"
warning: load: can't read `rho' (unknown datatype)
error: octave_base_value::load_binary(): wrong type argument `<unknown type>'
error: load: error while reading hdf5 item rho
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 47291026526976:
  #000: ../../../src/H5Gdeprec.c line 777 in H5Giterate(): group
iteration failed
    major: Symbol table
    minor: Iteration failed
  #001: ../../../src/H5G.c line 1532 in H5G_iterate(): error iterating
over links
    major: Symbol table
    minor: Iteration failed
  #002: ../../../src/H5Gobj.c line 599 in H5G_obj_iterate(): can't
iterate over symbol table
    major: Symbol table
    minor: Iteration failed
  #003: ../../../src/H5Gstab.c line 522 in H5G_stab_iterate():
iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #004: ../../../src/H5B.c line 1302 in H5B_iterate(): B-tree iteration failed
    major: B-Tree node
    minor: Iteration failed
  #005: ../../../src/H5B.c line 1225 in H5B_iterate_helper(): iterator
function failed
    major: B-Tree node
    minor: Unable to list node
  #006: ../../../src/H5Gnode.c line 1021 in H5G_node_iterate():
iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location


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