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

[Quentin Chevalier]

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)

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/