minor improvements to test scripts

Change-Id: I2827565c45cd6c66c0d1ffa1d6ecab18db4713f3
Fix hdf5 backend.

Have to call xdmf3array::read() to ensure contents are loaded into memory.
Added ifdefd out deepcopy option in process of debugging, and kept it
since it might be useful.

Change-Id: I85964eba08f6f92523e385a19f117840604e51cf