[petsc-users] Creating HDF5 groups

[Matthew Knepley]

On Mon, Nov 28, 2011 at 2:20 PM, Tim Gallagher <tim.gallagher at gatech.edu>wrote:

> Hi,
>
> I'm a little confused about why this section of code doesn't work, so
> hopefully somebody can help me. I'm able to run the
> vec/vec/examples/tutorials/ex19.c test that creates an HDF5 file, and
> h5dump verifies that it is making the groups and putting vectors in them.
> However, my code does not make the group (so it obviously doesn't put the
> vector in it!). The function is:
>

I commented out the write into the root group in ex19 and it worked fine:

knepley:/PETSc3/petsc/petsc-dev$ ./arch-sieve-fdatatypes-debug/bin/h5dump
./ex19.h5
./arch-sieve-fdatatypes-debug/bin/h5dump ./ex19.h5
HDF5 "./ex19.h5" {
GROUP "/" {
   GROUP "testBlockSize" {
      DATASET "TestVec" {
         DATATYPE  H5T_IEEE_F64LE
         DATASPACE  SIMPLE { ( 3, 2 ) / ( 3, 2 ) }
         DATA {
         (0,0): 1, 1,
         (1,0): 1, 1,
         (2,0): 1, 1
         }
      }
   }
   GROUP "testTimestep" {
      DATASET "TestVec" {
         DATATYPE  H5T_IEEE_F64LE
         DATASPACE  SIMPLE { ( 2, 3, 2 ) / ( H5S_UNLIMITED, 3, 2 ) }
         DATA {
         (0,0,0): 1, 1,
         (0,1,0): 1, 1,
         (0,2,0): 1, 1,
         (1,0,0): 1, 1,
         (1,1,0): 1, 1,
         (1,2,0): 1, 1
         }
      }
   }
}
}

   Matt


> #undef __FUNCT__
> #define __FUNCT__ "Body::SaveGrid"
> PetscErrorCode Body::SaveGrid(const char filename[])
> {
>  PetscViewer hdf5File;
>  Vec coordVec;
>
>  // Grab the coordinate vector
>  m_lastError = DMDAGetCoordinates(m_nodes,&coordVec);
>  CHKERRXX(m_lastError);
>
>  m_lastError = PetscObjectSetName((PetscObject) coordVec, "Coordinates");
>  CHKERRXX(m_lastError);
>
>  // Open the file
>  m_lastError = PetscViewerHDF5Open(m_commGroup, filename, FILE_MODE_WRITE,
> &hdf5File);
>  CHKERRXX(m_lastError);
>
>  // Set the group to dump the grid in
>  m_lastError = PetscViewerHDF5PushGroup(hdf5File, "/grid");
>  CHKERRXX(m_lastError);
>
>  // Dump the coordinates
>  m_lastError = VecView(coordVec, hdf5File);
>  CHKERRXX(m_lastError);
>
>  m_lastError = PetscViewerHDF5PopGroup(hdf5File);
>  CHKERRXX(m_lastError);
>
>  // Clean up
>  m_lastError = PetscViewerDestroy(&hdf5File);
>  CHKERRXX(m_lastError);
> }
>
> The only thing I can really see different about this and ex19 is that I
> don't first write any dataset to the root group, but that's not required to
> be valid HDF5. If I call PetscViewerHDF5GetGroup after the PushGroup call,
> it returns /grid.
>
> Any ideas?
>
> Thanks,
>
> Tim
>



-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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