[petsc-users] How to read/write a HDF5 file using petsc4py ?
Matthew Knepley
knepley at gmail.com
Mon Dec 6 14:39:21 CST 2021
On Mon, Dec 6, 2021 at 3:27 PM Quentin Chevalier <
quentin.chevalier at polytechnique.edu> wrote:
> 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
>
Did it find HDF5? If not, it will shut it off. You need to send us
$PETSC_DIR/configure.log
so we can see what happened in the configure run.
Thanks,
Matt
> * 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>
> >
> >
>
--
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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