[petsc-users] Loading external array data into PETSc

[Matthew Knepley]

On Thu, Mar 4, 2021 at 1:10 AM Smit Thijs <thijs.smit at hest.ethz.ch> wrote:

> Hi Matt, Roland and others,
>
>
>
> @ Roland, I can create the Vec in Petsc, but want to load it with external
> data. I can arrange that data in what ever way with Python. It is about two
> vectors, each of length 4.6 x10^6 entries.
>
>
>
> I have created a hdf5 file with Python and try to load it into PETSc which
> gives me some errors. I added the small test script I am using. The error I
> am getting is:
>
>
>
> error: ‘PetscViewerHDF5Open’ was not declared in this scope; did you mean
> ‘PetscViewerVTKOpen’?
>
>
>
> Am I using the wrong header
>

Did you configure PETSc with HDF5? If so, the configure.log will have an
entry for it at the bottom. If not, reconfigure with it:

  ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/conf/reconfigure-${PETSC_ARCH}.py
--download-hdf5

or you can use

  --with-hdf5-dir=/path/to/hdf5

if it is already installed.

  Thanks,

    Matt


> Best,
>
>
>
> Thijs
>
>
>
> *From:* Matthew Knepley <knepley at gmail.com>
> *Sent:* 03 March 2021 23:02
> *To:* Smit Thijs <thijs.smit at hest.ethz.ch>
> *Cc:* petsc-users at mcs.anl.gov
> *Subject:* Re: [petsc-users] Loading external array data into PETSc
>
>
>
> On Wed, Mar 3, 2021 at 4:23 PM Smit Thijs <thijs.smit at hest.ethz.ch> wrote:
>
> Hi All,
>
>
>
> I would like to readin a fairly large external vector into PETSc to be
> used further. My idea was to write a hdf5 file using Python with the vector
> data. Then read that hdf5 file into PETSc using PetscViewerHDF5Open and
> VecLoad. Is this the advised way or is there a better alternative to
> achieve the same (getting this external array data into PETSc)?
>
>
>
> I think there are at least two nice ways to do this:
>
>
>
> 1) Use HDF5. Here you have to name your vector to match the HDF5 object
>
>
>
> 2) Use raw binary. This is a specific PETSc format, but it is fast and
> simple.
>
>
>
>   Thanks,
>
>
>
>     Matt
>
>
>
> Best regards,
>
>
>
> Thijs Smit
>
>
>
> PhD Candidate
>
> ETH Zurich
>
> Institute for Biomechanics
>
>
>
>
>
>
> --
>
> 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/>
>


-- 
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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