Hi Matt, Thank you, I needed to reconfigure with hdf5.
The import works well now. Best, Thijs From: Matthew Knepley <knep...@gmail.com> Sent: 04 March 2021 14:53 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 Thu, Mar 4, 2021 at 1:10 AM Smit Thijs <thijs.s...@hest.ethz.ch<mailto:thijs.s...@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 <knep...@gmail.com<mailto:knep...@gmail.com>> Sent: 03 March 2021 23:02 To: Smit Thijs <thijs.s...@hest.ethz.ch<mailto:thijs.s...@hest.ethz.ch>> Cc: petsc-users@mcs.anl.gov<mailto: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/> -- 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/>