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.
Barry
> On Mar 18, 2016, at 2:50 PM, Barry Smith <[email protected]> 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
>
>
>
>
>
