[petsc-users] petsc4py error code 86 from ViewerHDF5().create

[Barry Smith]

   You need to ./configure PETSc for HDF5 using

> --with-fortran-bindings=0 --with-mpi-dir=/usr --download-hdf5

  It may need additional options, if it does then rerun the ./configure with the additional options it lists.


> On Mar 12, 2024, at 8:19 PM, adigitoleo (Leon) <adigitoleo at posteo.net> wrote:
> 
> This Message Is From an External Sender
> This message came from outside your organization.
> Hello,
> 
> I'm new to the list and have a limited knowledge of PETSc so far, but
> I'm trying to use a software (underworld3) that relies on petsc4py.
> I have built PETSc with the following configure options:
> 
>     --with-fortran-bindings=0 --with-mpi-dir=/usr
> 
> and `make test` gives me 160 failures which all seem to be timeouts or
> arising from my having insufficient "slots" (cores?). I subsequently
> built underworld3 with something like
> 
>     cd $PETSC_DIR
>     PETSC_DIR=... PETSC_ARCH=... NUMPY_INCLUDE=... pip install src/binding/petsc4py
>     cd /path/to/underworld3/tree
>     pip install h5py
>     pip install mpi4py
>     PETSC_DIR=... PETSC_ARCH=... NUMPY_INCLUDE=... pip install -e .
> 
> following their instructions. Building their python wheel/package was
> successful, however when I run their tests (using pytest) I get errors
> during test collection, which all come from petsc4py and have a stack
> trace that ends in the snippet attached below. Am I going about this
> wrong? How do I ensure that the HDF5 types are defined?
> 
>     src/underworld3/discretisation.py:86: in _from_gmsh
>         viewer = PETSc.ViewerHDF5().create(filename + ".h5", "w", comm=PETSc.COMM_SELF)
>     petsc4py/PETSc/Viewer.pyx:916: in petsc4py.PETSc.ViewerHDF5.create
>         ???
>     E   petsc4py.PETSc.Error: error code 86
>     ------------------------------- Captured stderr --------------------------------
>     [0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
>     [0]PETSC ERROR: Unknown type. Check for miss-spelling or missing package: https://urldefense.us/v3/__https://petsc.org/release/install/install/*external-packages__;Iw!!G_uCfscf7eWS!duVp7PZwdvHgymCgufX290k3tptJCHEo3vrV7dNt9zumYwqzDVsb1AG1HHargxq0LL-1JO6mjgiS7Vbykb1_siyXWw$
>     [0]PETSC ERROR: Unknown PetscViewer type given: hdf5
>     [0]PETSC ERROR: See https://urldefense.us/v3/__https://petsc.org/release/faq/__;!!G_uCfscf7eWS!duVp7PZwdvHgymCgufX290k3tptJCHEo3vrV7dNt9zumYwqzDVsb1AG1HHargxq0LL-1JO6mjgiS7Vbykb1LEFOicQ$ for trouble shooting.
>     [0]PETSC ERROR: Petsc Release Version 3.20.4, unknown
>     [0]PETSC ERROR: /home/leon/vcs/underworld3/.venv-underworld3/bin/pytest on a arch-linux-c-debug named roci by leon Wed Mar 13 00:01:33 2024
>     [0]PETSC ERROR: Configure options --with-fortran-bindings=0 --with-mpi-dir=/usr
>     [0]PETSC ERROR: #1 PetscViewerSetType() at /home/leon/vcs/petsc/src/sys/classes/viewer/interface/viewreg.c:535
> 
> Cheers,
> Leon

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