[petsc-users] How to read/write a HDF5 file using petsc4py ?

Lawrence Mitchell wence at gmx.li
Tue Dec 7 07:59:10 CST 2021

> On 7 Dec 2021, at 13:26, Quentin Chevalier <quentin.chevalier at polytechnique.edu> wrote:
> Ok my bad, that log corresponded to a tentative --download-hdf5. This
> log corresponds to the commands given above and has --with-hdf5 in its
> options.

OK, so PETSc is configured with HDF5. I assume you have now built it (with make as instructed)

You now need to _rebuild_ petsc4py to link against this new PETSc.

Something like

PETSC_DIR=/path/to/petsc PETSC_ARCH=whatever-arch pip install /path/to/petsc/src/binding/petsc4py

I note that the container build cleans out the source tree (see https://github.com/FEniCS/dolfinx/blob/main/docker/Dockerfile#L338), so I think that you have only rerun configure and not make (so you don't yet have a libpetsc that is appropriately linked).


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