[petsc-dev] HDF5 usage in PETSc without MPI? WTF? Totally broken?

[Matthew Knepley]

On Wed, Mar 23, 2016 at 2:28 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>   Jed and Matt and anyone else who understands the HDF5 viewer
>
>        No one has answered this. If I get no response  I am going to
> assume that PETSc requires HDF5 built with MPI and remove the #if defs in
> the code.
>

Are you sure that the Vec code fails when HDF5 is serial? I don't know what
happens when multiple
procs use H5Lexists() and friends. Maybe its transactional on the file. It
does use

   PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER));
#if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
  PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE));
#endif

If it does require MPI, then fine, take out the #ifdefs.

   Matt


>   Barry
>
> > On Mar 18, 2016, at 2:50 PM, Barry Smith <bsmith at mcs.anl.gov> wrote:
> >
> >
> >  I am confused about the usage of HDF5 from PETSc.
> >
> >   In hdf5.py
> >
> >  def configureLibrary(self):
> >    if self.libraries.check(self.dlib, 'H5Pset_fapl_mpio'):
> >      self.addDefine('HAVE_H5PSET_FAPL_MPIO', 1)
> >    return
> >
> >  So PETSc does not require HDF5 to have been built using MPI (for
> example if it was built by someone else without MPI.)
> >
> >  In PetscErrorCode  PetscViewerFileSetName_HDF5(PetscViewer viewer,
> const char name[])
> >
> > #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
> >  PetscStackCallHDF5(H5Pset_fapl_mpio,(plist_id,
> PetscObjectComm((PetscObject)viewer), info));
> > #endif
> >
> >  so it only sets collective IO if the symbol was found and hence HDF5
> was built for MPI
> >
> >  But in places like  VecView_MPI_HDF5(Vec xin, PetscViewer viewer)
> >
> >   it uses MPI as if it was collective? Though it might not be because
> hdf5 could have been built without MPI
> >
> >  So if I build PETSc with a non-MPI hdf5 and yet use the hdf5 viewer in
> parallel; do the generated hdf5 files contain garbage?
> >
> >  It seems to me we need to have hdf5.py REQUIRE the existence of
> H5Pset_fapl_mpio?
> >
> >  Barry
> >
> >
> >
> >
> >
>
>


-- 
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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