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

[Barry Smith]

> On Mar 23, 2016, at 7:35 PM, Matthew Knepley <knepley at gmail.com> wrote:
> 
> 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?

  How would I verify if the if the resulting hdf5 file is good or not?

 Barry

> 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