[petsc-users] Load Vec from 1D HDF5 dataset MATT READ THIS EMAIL!

[Matthew Knepley]

On Fri, Mar 20, 2015 at 12:08 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
> > On Mar 20, 2015, at 11:31 AM, Håkon Strandenes <haakon at hakostra.net>
> wrote:
> >
> > Yes, in the HDF5 file. Currently a dof=1 DMDA Vec is saved as a NZ x NY
> x NX dataset, wile a dof > 1 is saved as NZ x NY x NX x dof in the HDF5
> file.
>
>   Actually a 1d DMDA is stored as a NX dataset, a 2d DMDA is stored as a
> NY x NX data set and a 3d DMDA is stored as a NZ x NY x NX data set and an
> extra dimension is added if dof > 1.   And I think this is great and
> intuitively obvious for users.
>
>    I agree with Hakon and advocate NOT sticking the extra dimension in
> when bs is 1. Here is Matt's entire commit
>
>
>    maxDims[dim] = dims[dim];
>    chunkDims[dim] = dims[dim];
>    ++dim;
> -  if (bs > 1) {
> +  if (bs >= 1) {
>      dims[dim]    = bs;
>      maxDims[dim] = dims[dim];
>      chunkDims[dim] = dims[dim];
>    }
>    count[dim] = PetscHDF5IntCast(xin->map->n)/bs;
>    ++dim;
> -  if (bs > 1) {
> +  if (bs >= 1) {
>      count[dim] = bs;
>      ++dim;
>    }
>    }
>    offset[dim] = PetscHDF5IntCast(low/bs);
>    ++dim;
> -  if (bs > 1) {
> +  if (bs >= 1) {
>      offset[dim] = 0;
>      ++dim;
>    }
>
>   (Then there is Karl's one line fix for reading HDF5 files.)
>
>   Arguing that handling bs = 1 as a special case greatly (or even
> modestly) increases the complexity of the PETSc source code is nonsense.
>
>   So I want a stronger case presented then
>
> >> My rationale was to simplify our code path, and have one way to handle
> fields with components. I did not
> >> want to special case a field with one component.
>

If we special case here, we must special case in everything we do, such as
automatic generation of Xdmf.
I would rather say that the PETSc format always has the bs in it, which
makes it easier to process and
consistent. However, we allowing reading of of a set without blocksize.

We would have the ability to write without blocksize by setting the
blocksize to -1.

   Matt


>   otherwise I think we should undo Matt's change.
>
>   Barry
>
>
>
> >
> > In my humble opinion, it is best to leave the DMDA's as it is, and fix
> up the code related to the plain Vecs. That code is already full of "if (bs
> >= 1) dim++" etc. which is useless (as Barry points out).
> >
> > My final point is that one should handle this in a CONSISTENT manner for
> both "plain Vecs" and "DMDA Vecs", i.e. decide wither one want to always
> add one dimension for bs and dof or leave that dimension out for the
> special case with bs=1/dof=1.
> >
> > Håkon
> >
> >
> > On 20. mars 2015 16:57, Jed Brown wrote:
> >> Håkon Strandenes <haakon at hakostra.net> writes:
> >>> I mean that if you decide to stick with the current way of
> >>> reading/writing a "plain 1D" Vec with N elements as a N x 1
> >>> array/dataset, you should treat a dof=1 DMDA Vec as an NZ x NY x NX x 1
> >>> array/dataset.
> >>
> >> In the HDF5 file?  I agree.
> >>
>
>


-- 
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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