[petsc-users] Error loading data coming from a .hdf5 file into a DMSwarm

[Matthew Knepley]

On Mon, Apr 1, 2024 at 11:13 AM MIGUEL MOLINOS PEREZ <mmolinos at us.es> wrote:

> Dear Matthew,
>
> Thank you for your suggestion. I tried to update the vector with the
> information coming from the hdf5 file inside the main function. Then I
> print the vector two times (see the lines below), the first time it has the
> correct data. However, the second time, it has the same values like I never
> updated it with VecLoad.
>
> It is an alternative way of initialise a vector coming from DMSWarm with
> previously stored information (keeping the parallel structure)?
>

Oh, you cannot use the Swarm vectors for VecLoad(). They are just a view
into the particle data, and that view is destroyed on restore. Swarm data
is stored in a particle-like data structure, not in Vecs. If you want to
load this Vec, you have to duplicate exactly as you did. This interface is
likely to change in the next year to make this problem go away.

  Thanks,

    Matt


> Miguel
>
> //! Load Hdf5 viewer
> PetscViewer viewer_hdf5;
> REQUIRE_NOTHROW(PetscViewerHDF5Open(MPI_COMM_WORLD, Output_hdf5_file,
> FILE_MODE_READ, &viewer_hdf5));
> REQUIRE_NOTHROW(PetscViewerHDF5PushTimestepping(viewer_hdf5));
>
> //! Load the vector and fill it with the information from the .hdf5 file
> Vec stdv_q;
> REQUIRE_NOTHROW(DMSwarmCreateGlobalVectorFromField(
> Simulation.atomistic_data, "stdv-q", &stdv_q));
>
> REQUIRE_NOTHROW(PetscViewerHDF5PushGroup(viewer_hdf5, "/particle_fields"
> ));
> REQUIRE_NOTHROW(VecLoad(stdv_q, viewer_hdf5));
> REQUIRE_NOTHROW(VecView(stdv_q, PETSC_VIEWER_STDOUT_WORLD));
> REQUIRE_NOTHROW(PetscViewerHDF5PopGroup(viewer_hdf5));
>
> REQUIRE_NOTHROW(DMSwarmDestroyGlobalVectorFromField(
> Simulation.atomistic_data, "stdv-q", &stdv_q));
>
> //! Destoy HDF5 context
> REQUIRE_NOTHROW(PetscViewerDestroy(&viewer_hdf5));
>
> //! Load the vector again and print
> REQUIRE_NOTHROW(DMSwarmCreateGlobalVectorFromField(
> Simulation.atomistic_data, "stdv-q", &stdv_q));
>
> REQUIRE_NOTHROW(VecView(stdv_q, PETSC_VIEWER_STDOUT_WORLD));
>
> REQUIRE_NOTHROW(DMSwarmDestroyGlobalVectorFromField(
> Simulation.atomistic_data, "stdv-q", &stdv_q));
>
> Best,
> Miguel
>
> Miguel Molinos
> Investigador postdoctoral
> Juan de la Cierva
> Dpto. Mecánica de Medios Continuos y Teoría de Estructuras - ETSI
> Universidad de Sevilla
> Camino de los descubrimientos, s/n
> 41092 Sevilla
>
>
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>
>
> On 1 Apr 2024, at 16:28, Matthew Knepley <knepley at gmail.com> wrote:
>
> From the description, my guess is that this is pointer confusion. The
> vector inside the function is different from the vector outside the
> function.
>
>
>

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