Re: [petsc-users] Loading external array data into PETSc

[Smit Thijs]

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?

Best,

Thijs

From: Matthew Knepley <knep...@gmail.com>
Sent: 03 March 2021 23:02
To: Smit Thijs <thijs.s...@hest.ethz.ch>
Cc: petsc-users@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.s...@hest.ethz.ch<mailto:thijs.s...@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/>

#include <petsc.h>
#include <petscvec.h>
#include <petscviewerhdf5.h>

static char help[] = "Test HDF5\n\n";

int main(int argc, char* argv[]) {

    // Error code for debugging
    PetscErrorCode ierr;

    // Initialize PETSc / MPI and pass input arguments to PETSc
    PetscInitialize(&argc, &argv, PETSC_NULL, help);

    Vec xPassive;
    VecCreate(PETSC_COMM_WORLD, &xPassive);
    PetscObjectSetName((PetscObject) xPassive, "xPassive");
    VecSetSizes(xPassive, PETSC_DECIDE, 4614720);
    VecSetFromOptions(xPassive);

    PetscViewer viewin;
    
    PetscViewerHDF5Open(PETSC_COMM_WORLD, "xPassive.h5", FILE_MODE_READ, 
&viewin);
        
    PetscViewerDestroy(&viewin);
    VecDestroy(&xPassive);
    
    PetscFinalize();
    return 0;
}