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

[MIGUEL MOLINOS PEREZ]

Dear Matthew,

I came up with a workaround for the problem. I duplicate the vector and use the duplicated copy to read the information from the hdf5 file. Then I swap both vectors and delete the copy. If I invoke VecView outside of the function, the value has been modified properly. However, this solution seems a little bit “ugly”. I share it just in case someone is facing a similar problem or it can help to understand what is going wrong with my previous implementation.

Best,
Miguel

Vec stdv_q;
PetscCall(DMSwarmCreateGlobalVectorFromField(Simulation->atomistic_data,
"stdv-q", &stdv_q));

Vec stdv_q_hdf5;
PetscCall(VecDuplicate(stdv_q, &stdv_q_hdf5));
PetscCall(PetscObjectSetName((PetscObject)stdv_q_hdf5,
"DMSwarmSharedField_stdv-q"));

PetscCall(VecLoad(stdv_q_hdf5, viewer_hdf5));

PetscCall(VecSwap(stdv_q, stdv_q_hdf5));
PetscCall(VecDestroy(&stdv_q_hdf5));

PetscCall(DMSwarmDestroyGlobalVectorFromField(Simulation->atomistic_data,
"stdv-q", &stdv_q));

On 1 Apr 2024, at 17:13, Miguel Molinos <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)?

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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