[petsc-dev] MPI Vec and HDF5 output

[Matthew Knepley]

On Fri, Jan 28, 2011 at 5:08 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>  Is there anyway we can get this into the petsc-dev source so it is fixed
> for everyone in the future?
>

Brad already pushed it :)

    Matt


>   Thanks
>
>   Barry
>
> On Jan 28, 2011, at 2:54 PM, Brad Aagaard wrote:
>
> > Barry-
> >
> > It turns out the workaround was explained deep in some of the HDF5
> documentation. I pushed the fix. If the local Vec size is zero, then I
> created a null memspace and reset the filespace to none.
> >
> > Brad
> >
> >
> > On 01/28/2011 10:00 AM, Barry Smith wrote:
> >>
> >>   Sounds like a bug report/inquiry to HDF5 folks.
> >>
> >>    Barry
> >>
> >>
> >> On Jan 28, 2011, at 10:23 AM, Brad Aagaard wrote:
> >>
> >>> We are trying to get HDF5 output working in PyLith using the PETSc HDF5
> viewer. I get an HDF5 error
> >>>
> >>> H5Screate_simple(): zero sized dimension for non-unlimited dimension,
> >>> VecView_MPI_HDF5() line 771 in petsc-dev/src/vec/vec/impls/mpi/pdvec.c
> >>>
> >>> when I have a Vec that has a zero local size on a processor (the global
> size is nonzero). The Vec layout is correct in that we expect some
> processors to have a local size of zero (the field is over only a portion of
> the domain).
> >>>
> >>> The collective write of the Vec creates the filespace using the global
> size and the memspace using the local size. It is in trying to create the
> memspace that the error occurs. I tried adjusting pdvec.c so that it creates
> a null memspace when the local size is zero but then I get an error during
> the write about differences in dimensions (the number of dimensions in the
> filespace and memspace don't agree). I was unable to find any info on this
> type of use case in the HDF5 documentation.
> >>>
> >>> I have attached a toy example that illustrates the problem.
> >>> mpiexec -n 1 test_view [creates the expected test.h5 file]
> >>> mpiexec -n 2 test_view [generates the above error]
> >>>
> >>> Thanks,
> >>> Brad
> >>> <test_view.tgz>
> >>
> >>
> >
>
>


-- 
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.mcs.anl.gov/pipermail/petsc-dev/attachments/20110128/f9060ac0/attachment.html>