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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
