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

Mon Dec 6 14:27:11 CST 2021

Fine. MWE is unchanged :
* Run this docker container <https://hub.docker.com/r/dolfinx/dolfinx>
* Do : python3 -c "from petsc4py import PETSc;
PETSc.Viewer().createHDF5('dummy.h5')"

Updated attempt at a fix :
* cd /usr/local/petsc/
* ./configure PETSC_ARCH= linux-gnu-real-32  PETSC_DIR=/usr/local/petsc
--with-hdf5 --force
* make PETSC_DIR=/usr/local/petsc PETSC-ARCH= linux-gnu-real-32 all

Still no joy. The same error remains.

Quentin

On Mon, 6 Dec 2021 at 20:04, Pierre Jolivet <pierre at joliv.et> wrote:
>
>
>
> On 6 Dec 2021, at 7:42 PM, Quentin Chevalier <
quentin.chevalier at polytechnique.edu> wrote:
>
> The PETSC_DIR exactly corresponds to the previous one, so I guess that
rules option b) out, except if a specific option is required to overwrite a
previous installation of PETSc. As for a), well I thought reconfiguring
pretty direct, you're welcome to give me a hint as to what could be wrong
in the following process.
>
> Steps to reproduce this behaviour are as follows :
> * Run this docker container
> * Do : python3 -c "from petsc4py import PETSc;
PETSc.Viewer().createHDF5('dummy.h5')"
>
> After you get the error Unknown PetscViewer type, feel free to try :
>
> * cd /usr/local/petsc/
> * ./configure --with-hfd5
>
>
> It’s hdf5, not hfd5.
> It’s PETSC_ARCH, not PETSC-ARCH.
> PETSC_ARCH is missing from your configure line.
>
> Thanks,
> Pierre
>
> * make PETSC_DIR=/usr/local/petsc PETSC-ARCH=linux-gnu-real-32 all
>
> Then repeat the MWE and observe absolutely no behavioural change
whatsoever. I'm afraid I don't know PETSc well enough to be surprised by
that.
>
> Quentin
>
>
>
> Quentin CHEVALIER – IA parcours recherche
>
> LadHyX - Ecole polytechnique
>
> __________
>
>
>
> On Mon, 6 Dec 2021 at 19:24, Matthew Knepley <knepley at gmail.com> wrote:
>>
>> On Mon, Dec 6, 2021 at 1:22 PM Quentin Chevalier <
quentin.chevalier at polytechnique.edu> wrote:
>>>
>>> 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.
>>
>>
>> If you reconfigured and rebuilt, it is impossible to get the same error,
so
>>
>>   a) You did not reconfigure
>>
>>   b) Your new build is somewhere else on the machine
>>
>>   Thanks,
>>
>>      Matt
>>
>>>
>>> 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/
>>
>>
>>
>> --
>> 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/
>
> <image003.jpg>
>
>
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