[petsc-users] How to read/write a HDF5 file using petsc4py ?

[Matthew Knepley]

On Mon, Dec 6, 2021 at 1:08 PM Quentin Chevalier <
quentin.chevalier at polytechnique.edu> wrote:

> Hello Matthew and thanks for your quick response.
>
> I'm afraid I did try to snoop around the container and rerun PETSc's
> configure with the --with-hdf5 option, to absolutely no avail.
>
> I didn't see any errors during config or make, but it failed the tests
> (which aren't included in the minimal container I suppose)
>

Failed which tests? What was the error?

  Thanks,

    Matt


> Quentin
>
>
>
> Quentin CHEVALIER – IA parcours recherche
>
> LadHyX - Ecole polytechnique
>
> __________
>
>
>
> On Mon, 6 Dec 2021 at 19:02, Matthew Knepley <knepley at gmail.com> wrote:
> >
> > On Mon, Dec 6, 2021 at 11:28 AM Quentin Chevalier <
> quentin.chevalier at polytechnique.edu> wrote:
> >>
> >> Hello PETSc users,
> >>
> >> This email is a duplicata of this gitlab issue, sorry for any
> inconvenience caused.
> >>
> >> I want to compute a PETSc vector in real mode, than perform
> calculations with it in complex mode. I want as much of this process to be
> parallel as possible. Right now, I compile PETSc in real mode, compute my
> vector and save it to a file, then switch to complex mode, read it, and
> move on.
> >>
> >> This creates unexpected behaviour using MPIIO, so on Lisandro Dalcinl's
> advice I'm moving to HDF5 format. My code is as follows (taking inspiration
> from petsc4py doc, a bitbucket example and another one, all top Google
> results for 'petsc hdf5') :
> >>>
> >>> viewer = PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD)
> >>> q.load(viewer)
> >>> q.ghostUpdate(addv=PETSc.InsertMode.INSERT,
> mode=PETSc.ScatterMode.FORWARD)
> >>
> >>
> >> This crashes my code. I obtain traceback :
> >>>
> >>>   File "/home/shared/code.py", line 121, in Load
> >>>     viewer = PETSc.Viewer().createHDF5(file_name, 'r', COMM_WORLD)
> >>>   File "PETSc/Viewer.pyx", line 182, in
> petsc4py.PETSc.Viewer.createHDF5
> >>> petsc4py.PETSc.Error: error code 86
> >>> [0] PetscViewerSetType() at
> /usr/local/petsc/src/sys/classes/viewer/interface/viewreg.c:442
> >>> [0] Unknown type. Check for miss-spelling or missing package:
> https://petsc.org/release/install/install/#external-packages
> >>> [0] Unknown PetscViewer type given: hdf5
> >
> > This means that PETSc has not been configured with HDF5 (--with-hdf5 or
> --download-hdf5), so the container should be updated.
> >
> >   THanks,
> >
> >     Matt
> >
> >>
> >> I have petsc4py 3.16 from this docker container (list of dependencies
> include PETSc and petsc4py).
> >>
> >> I'm pretty sure this is not intended behaviour. Any insight as to how
> to fix this issue (I tried running ./configure --with-hdf5 to no avail) or
> more generally to perform this jiggling between real and complex would be
> much appreciated,
> >>
> >> Kind regards.
> >>
> >> Quentin
> >
> >
> >
> > --
> > 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
> >
> > https://www.cse.buffalo.edu/~knepley/
>


-- 
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

https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>
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