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

[Quentin Chevalier]

It failed all of the tests included in `make
PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 check`, with
the error `/usr/bin/bash: line 1: cd: src/snes/tutorials: No such file
or directory`

I am therefore fairly confident this a "file absence" problem, and not
a compilation problem.

I repeat that there was no error at compilation stage. The final stage
did present `gmake[3]: Nothing to be done for 'libs'.` but that's all.

Again, running `./configure --with-hdf5` followed by a `make
PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 all` does not
change the problem. I get the same error at the same position as
before.

I will comment I am running on OpenSUSE.

Quentin

On Mon, 6 Dec 2021 at 19:09, Matthew Knepley <knepley at gmail.com> wrote:
>
> 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/